Marker assisted selection in plant breeding

Marker assisted selection (MAS) is ‘smart breeding’ or fast track plant breeding technology. It is one tool utilized in breeding companies and research institutes for fast development of improved varieties, giving possibility to select desirable traits more directly using DNA markers. In this review, we discussed the use of MAS in biotic, abiotic, quality and other agronomic traits. Besides, we emphasized the importance of MAS at ICARDA and underlined the successful application of MAS in the last 10 years. The use of molecular markers makes the process of selecting parental lines more efficient based on genetic diversity analysis. It can aid the conventional breeding, especially for certain biotic and abiotic traits laborious to manage. Still, MAS contributed very little to the release of improved cultivars with greater tolerance to abiotic stresses, with only a few exceptions. MAS was extensively used to improve rice varieties, mainly resistant to bacterial blight and blast disease and was applied in drought tolerance along with GPC (Grain protein content) in quality traits. MAS at ICARDA is used to characterize new parental materials for disease resistance genes as well as in screening advanced lines with a focus on association mapping and identification of new QTLs. The application of MAS increased in the last decade. It is more and more used in different crops. However, rice is still the dominant crop in terms of number of publications using MAS. Keywords: marker assisted selection, plant, biotic stress, abiotic stress, quality, ICARD

Phenotypic and genetic diversity in Sinorhizobium meliloti and S. medicae from drought and salt affected regions of Morocco

<p>Abstract</p> <p>Background</p> <p><it>Sinorhizobium meliloti </it>and <it>S. medicae </it>are symbiotic nitrogen fixing bacteria in root nodules of forage legume alfalfa (<it>Medicago sativa </it>L.). In Morocco, alfalfa is usually grown in marginal soils of arid and semi-arid regions frequently affected by drought, extremes of temperature and soil pH, soil salinity and heavy metals, which affect biological nitrogen fixing ability of rhizobia and productivity of the host. This study examines phenotypic diversity for tolerance to the above stresses and genotypic diversity at Repetitive Extragenic Pallindromic DNA regions of <it>Sinorhizobium </it>nodulating alfalfa, sampled from marginal soils of arid and semi-arid regions of Morocco.</p> <p>Results</p> <p><it>Rsa</it>I digestion of PCR amplified 16S rDNA of the 157 sampled isolates, assigned 136 isolates as <it>S. meliloti </it>and the rest as <it>S. medicae</it>. Further phenotyping of these alfalfa rhizobia for tolerance to the environmental stresses revealed a large degree of variation: 55.41%, 82.16%, 57.96% and 3.18% of the total isolates were tolerant to NaCl (>513 mM), water stress (-1.5 MPa), high temperature (40°C) and low pH (3.5), respectively. Sixty-seven isolates of <it>S. meliloti </it>and thirteen isolates of <it>S. medicae</it> that were tolerant to salinity were also tolerant to water stress. Most of the isolates of the two species showed tolerance to heavy metals (Cd, Mn and Zn) and antibiotics (chloramphenicol, spectinomycin, streptomycin and tetracycline). The phenotypic clusters observed by the cluster analysis clearly showed adaptations of the <it>S. meliloti </it>and <it>S. medicae </it>strains to the multiple stresses. Genotyping with rep-PCR revealed higher genetic diversity within these phenotypic clusters and classified all the 157 isolates into 148 genotypes. No relationship between genotypic profiles and the phenotypes was observed. The Analysis of Molecular Variance revealed that largest proportion of significant (P < 0.01) genetic variation was distributed within regions (89%) than among regions (11%).</p> <p>Conclusion</p> <p>High degree of phenotypic and genotypic diversity is present in <it>S. meliloti </it>and <it>S. medicae </it>populations from marginal soils affected by salt and drought, in arid and semi-arid regions of Morocco. Some of the tolerant strains have a potential for exploitation in salt and drought affected areas for biological nitrogen fixation in alfalfa.</p

Amélioration de la production des plantes haploïdes et haploïdes doublés utilisant la culture des anthères du blé

La production des plantes haploïdes et haploïdes doublés, fournit aux sélectionneurs du blé un moyen très efficace pour accélérer la production des lignées homozygotes. La culture des anthères est un parmi les processus d’induction et de régénération des haploïdes et des haploïdes doublés à partir des gamètes mâles. Son haut potentiel de production des plantes haploïdes et son applicabilité chez nombreuses espèces rendent cette technique remarquablement utilisable dans l’amélioration des plantes et l’exploitation commerciales des haploïdes doublés. De ce fait, l’objectif de cette revue est de discuter les publications les plus récentes sur l’amélioration de la culture des anthères de blé et les comparer aux résultats plus ou moins anciens. Ces publications seront d’une grande utilité dans l’amélioration du rendement des plantes haploïdes et haploïdes doublés et ils vont contribuer à faciliter les prochains travaux sur la culture des anthères. Mots clés: Blé, culture des anthères, haploïdes, haploïdes doublés, amélioration génétique.The production of haploids and double haploids, are widely used techniques in advanced breeding programs to speed-up the production of homozygote lines. Anther culture is one of the processes of induction and regeneration of haploids and double haploids from male gametic cells. Due to its high effectiveness and applicability in numerous plant species, it has outstanding potential for plant breeding and commercial exploitation of double haploids. Therefore, the objective of this revue is to discuss recent publications on improvement of wheat anther culture and compare it with older literature. Those publications will be of great utility in yield improvement of haploid and double haploid plants and will contribute for future research on anthers culture. Keywords: Wheat, anther culture, haploids, doubled haploids, genetic improvement

Data collection protocol

This document shows the data collection protocol to perform the sustainability assessment of different 4CE-MED cropping systems by applying life cycle thinking methodologies. Within 4CE-MED project, WP4 will select 3 countries and trials will be selected to compare the sustainability performance of current situations with the introduction of 4CE-MED cropping systems. The cases will belong to three major camelina cropping models presented in the project: Model A introduces Camelina to replace fallow in winter cereal sole-cropping systems, in marginal areas with very dry climate; Model B considers Camelina as a double-cropping cultivation in autumn, to precede typical Mediterranean summer crops; and Model C uses Camelina as a double-cropping in late spring/early summer in colder areas to follow winter pulses (e.g. pea) or cereals harvested as fodder. The selected cases would have followed the experimental protocol presented in WP2. This protocol is based on the Methodological framework to develop life cycle thinking assessment on 4CE-MED systems (D4.1). A literature review was also conducted for this deliverable, which allowed to observe there is limited LCA, E-LCC and S-LCA studies of the Camelina crop in Mediterranean regions. Most of the information found is referred to the application of Camelina as biofuel, while some articles even highlighted that camelina is not used as food. The definition of a goal and scope, expressed in the methodological framework for the assessment, expects to conduct a cradle-to-farm gate assessment with functionality based mostly on yield, and a perspective based on the crop succession. Functional unit is expected to be mass based, with derivations towards the environmental, economic and social impact categories of interest. The environmental dimension will refer to midpoint categories, with a consistent use as in most of the studies of Global Warming Potential, Eutrophication Potential and Terrestrial Acidification Potential. Regarding the economic dimension, cost categories, income and net margin will be observed, and the social dimension will include impact categories that range from endpoint to midpoint categories, where human rights, working conditions and community are to be addressed

Identification of quantitative trait loci controlling root and shoot traits associated with drought tolerance in a lentil (Lens culinaris Medik.) recombinant inbred line population

Drought is one of the major abiotic stresses limiting lentil productivity in rainfed production systems. Specific rooting patterns can be associated with drought avoidance mechanisms that can be used in lentil breeding programs. In all, 252 co-dominant and dominant markers were used for Quantitative Trait Loci (QTL) analysis on 132 lentil recombinant inbred lines based on greenhouse experiments for root and shoot traits during two seasons under progressive drought-stressed conditions. Eighteen QTLs controlling a total of 14 root and shoot traits were identified. A QTL-hotspot genomic region related to a number of root and shoot characteristics associated with drought tolerance such as dry root biomass, root surface area, lateral root number, dry shoot biomass and shoot length was identified. Interestingly, a QTL (QRSratioIX-2.30) related to root-shoot ratio, an important trait for drought avoidance, explaining the highest phenotypic variance of 27.6 and 28.9% for the two consecutive seasons, respectively, was detected. This QTL was closed to the co-dominant SNP marker TP6337 and also flanked by the two SNP TP518 and TP1280. An important QTL (QLRNIII-98.64) related to lateral root number was found close to TP3371 and flanked by TP5093 and TP6072 SNP markers. Also, a QTL (QSRLIV-61.63) associated with specific root length was identified close to TP1873 and flanked by F7XEM6b SRAP marker and TP1035 SNP marker. These two QTLs were detected in both seasons. Our results could be used for marker-assisted selection in lentil breeding programs targeting root and shoot characteristics conferring drought avoidance as an efficient alternative to slow and labor-intensive conventional breeding methods

Agro-morphological variability in durum wheat landraces of Morocco

Abstract The knowledge about the extent of variability, the distribution and the relationship between descriptors within local germplasm collection are a high value for the improvement and the efficient genetic diversity maintenance and utilization of plant species. The objective of this study was to evaluate the agro-morphological variability in a set of Moroccan durum wheat germplasm collection maintained in the National Gene Bank of Morocco (INRA, Settat). 467 durum wheat (Triticum turgidum L. var. durum) accessions comprising 444 landraces and 23 improved varieties were planted under field condition and their agro-morphological characters such as days to emergence, days to tillering, days to booting, days to head emergence, days to flowering, days to physiological maturity, plant height, thousands kernel weight, spike shape, and spike density were recorded. Univariate and multivariate analysis of data indicated that thousands kernel weight and plant height presented the highest coefficient of variation with 15.72% and 15.15% respectively. The two-dimensional principal coordinates analysis (2D PCOA) explained 52% of the total variance in the collection and separated the accessions into three main groups, namely, the early maturing and shorter (81 accessions), the moderately late and taller (154 accessions), and the late maturing and taller (232 accessions). The frequency distribution of spike characters showed the prevalence of the pyramidal and the dense spike with 54% and 42% respectively. The results of this study will support efforts of conservation and utilization of landraces in durum wheat breeding programmes

Development of specific primers for the detection of HVA1 from barley in transgenic durum wheat by polymerase chain reaction (PCR) technology

Genetic transformation is a widely employed tool in both basic research and commercial plant breeding programs. Its application requires that transgenes be stably integrated and expressed in the plant genome. When transgenic plants are developed, it is essential to determine which plants contain the transgene. Detection methods are usually based on amplification of the target transgene. This paper describes a development of detection method based on conventional and real time polymerase chain reaction (PCR) for simultaneous detection of barley HVA1 transgene and its transcript in transformed durum wheat. Since there exist a high homology between the barley HVA1 gene and the wheat gene, development of a specific sets of primers is needed for PCR-based characterizations, and the study of the transgene. Based on the alignment of the two genes sequences obtained from public databases, several primers were designed to detect and distinguish between the transformed and non-transformed plants. Real time PCR has been employed because of its inherent sensitivity and quantitative nature. It has been possible to design the following primers pairs F2/MMR, F2/R10 and F14/R10 as highly specific and suitable for the detection of HVA1 DNA by conventional and real-time PCR. Nonetheless, the primers used were allowed to reach high efficiencies and did not show any cross-reactivity with DNAs extracted from various plants. The sensitivity achieved was 6.4 pg. The primer pair F2/R10 was considered as highly specific for the detection of both DNA and mRNA of the HVA1 by real-time PCR. The assays proved to be accurate, specific, sensitive and sufficiently reproducible for further application in high-throughput molecular characterization of transgenic lines.Keywords: HVA1, durum wheat, transgenic plant, real time polymerase chain reaction (PCR), droughtAfrican Journal of Biotechnology, Vol. 13(4), pp. 581-592, 22 January, 201

Molecular variance and population structure of lentil (Lens culinaris Medik.) landraces from Mediterranean countries as revealed by simple sequence repeat DNA markers : implications for conservation and use

The Mediterranean region has a rich history of domestication and cultivation of lentil (Lens culinaris Medik.). Landraces have been grown and repeatedly selected by local farmers under different agro-environments. Characterization of molecular variation and genetic differentiation helps to ensure enhanced valorization, conservation and use of these genetic resources. Nineteen Simple Sequence Repeat DNA markers were used for molecular variance analysis (AMOVA) and population structure assessment underlying 74 lentil landraces from four Mediterranean countries: Morocco, Italy, Greece and Turkey. Based on AMOVA, presence of population structure and genetic differentiation at different levels were evidenced. Genetic diversity among Turkish landraces was higher than that of other countries. These landraces were more homogeneous as shown by low genetic differentiation among individuals within each landrace. Whereas Moroccan landraces followed by Italian and Greek provenances showed higher diversity and differentiation among individuals within landraces. The wide genetic variability of these landraces could help to better adaptation to biotic and abiotic stresses. Moreover, they could provide useful alleles related to adaptive traits for breeding purposes. Based on structure analysis, we obtained indications of possible presence of two major gene pools: a northern gene pool composed of Turkish, Italian and Greek landraces, and a southern gene pool composed of Moroccan landraces. Our results could be of interest when designing future diversity studies, collection missions, conservation and core collection construction strategies on Mediterranean lentil landraces

Genetic structure, diversity, and allelic richness in composite collection and reference set in chickpea (Cicer arietinum L.)

<p>Abstract</p> <p>Background</p> <p>Plant genetic resources (PGR) are the basic raw materials for future genetic progress and an insurance against unforeseen threats to agricultural production. An extensive characterization of PGR provides an opportunity to dissect structure, mine allelic variations, and identify diverse accessions for crop improvement. The Generation Challenge Program <url>http://www.generationcp.org</url> conceptualized the development of "composite collections" and extraction of "reference sets" from these for more efficient tapping of global crop-related genetic resources. In this study, we report the genetic structure, diversity and allelic richness in a composite collection of chickpea using SSR markers, and formation of a reference set of 300 accessions.</p> <p>Results</p> <p>The 48 SSR markers detected 1683 alleles in 2915 accessions, of which, 935 were considered rare, 720 common and 28 most frequent. The alleles per locus ranged from 14 to 67, averaged 35, and the polymorphic information content was from 0.467 to 0.974, averaged 0.854. Marker polymorphism varied between groups of accessions in the composite collection and reference set. A number of group-specific alleles were detected: 104 in Kabuli, 297 in desi, and 69 in wild <it>Cicer</it>; 114 each in Mediterranean and West Asia (WA), 117 in South and South East Asia (SSEA), and 10 in African region accessions. Desi and kabuli shared 436 alleles, while wild <it>Cicer </it>shared 17 and 16 alleles with desi and kabuli, respectively. The accessions from SSEA and WA shared 74 alleles, while those from Mediterranean 38 and 33 alleles with WA and SSEA, respectively. Desi chickpea contained a higher proportion of rare alleles (53%) than kabuli (46%), while wild <it>Cicer </it>accessions were devoid of rare alleles. A genotype-based reference set captured 1315 (78%) of the 1683 composite collection alleles of which 463 were rare, 826 common, and 26 the most frequent alleles. The neighbour-joining tree diagram of this reference set represents diversity from all directions of the tree diagram of the composite collection.</p> <p>Conclusion</p> <p>The genotype-based reference set, reported here, is an ideal set of germplasm for allele mining, association genetics, mapping and cloning gene(s), and in applied breeding for the development of broad-based elite breeding lines/cultivars with superior yield and enhanced adaptation to diverse environments.</p

Morphological characterization and pathogenicity of nine Fusarium spp. isolates collected from barley seeds (Hordeum vulgare L.) in Morocco

Barley (Hordeum vulgare L.) is the most produced and consumed grain in the world, and is an important source of food, forage and livestock feed in many developing countries including Morocco. Fusarium head blight (FHB) is one of the main fungal diseases of grain crops such as wheat, barley and maize caused by different species of the genus Fusarium. The FHB species complex produces mycotoxins that affect livestock feed, the baking, milling quality of wheat, the malting and brewing qualities of malt barley. Nine isolates of Fusarium spp. causing necrosis with typical FHB symptoms were isolated from infected barley genotypes planted at ICARDA’s Merchouch station, Rabat, Morocco. After seeds harvesting, all nine FHB isolates were purified and morphologically identified by characterizing their culture appearance (colony color, texture, form, and margin), shape and size of the macroconidia, and presence or absence of microconidia. Pathogenicity of these isolates was studied under controlled conditions using two inoculation methods (soil inoculation and hydroponic culture) on 12 barley varieties (Flinders, Litmus, Oxford, Commander, Latrobe, Vlaming, Fleet, Granger, Rosalind, Buloke, Keel and Campus). Morphological characterization using the Leslie and Summerell key, implied 5 different macroscopic and microscopic morphologies very similar to: Fusarium acuminatum (two isolates), F. crookwellense (two isolates), F. avenaceum (two isolates), F. sambucinum (one isolate) and Fusarium culmorum (two isolates). All 9 isolates caused FHB symptoms on all 12 barley varieties tested in both inoculation methods and the number of infected spikelets was assessed. Four barley varieties (Keel, Buloke, Latrobe and Commander) showed a heavy fungal infection (infected spikelet over 65%) and were considered susceptible to infection with the disease. Whereas, four barley varieties (Campus, Oxford, Vlaming and Granger) were resistant to the nine isolates compared to the other barley varieties (infected spikelet less than 35%). In addition, a significant difference (P < 0.05) was observed between Fusarium species