Genetic relationships among melon breeding lines revealed by RAPD markers and agronomic traits

 RAPD markers and agronomic traits were used to determine the genetic relationships among 32 breeding lines of melon belonging to seven varietal types. Most of the breeding lines were Galia and Piel de Sapo genotypes, which are currently being used in breeding programmes to develop new hybrid combinations. A total of 115 polymorphic reliable bands from 43 primers and 24 agronomic traits were scored for genetic distance calculations and cluster analysis. A high concordance between RAPDs and agronomic traits was observed when genetic relationships among lines were assessed. In addition, RAPD data were highly correlated with the pedigree information already known for the lines and revealed the existence of two clusters for each varietal type that comprised the lines sharing similar agronomic features. These groupings were consistent with the development of breeding programmes trying to generate two separate sets of parental lines for hybrid production. Nevertheless, the performance of certain hybrids indicated that RAPDs were more suitable markers than agronomic traits in predicting genetic distance among the breeding lines analysed. The employment of RAPDs as molecular markers both in germplasm management and improvement, as well as in the selection of parental lines for the development of new hybrid combinations, is discussed. Received: 25 July 1997 / Accepted: 6 October 1997     

Variation in monoculture and in mixture for grain yield and other characters in spring barley

Fourteen north-west European spring barley cultivars were grown alone or in binary mixtures sampled according to a partial diallel scheme. On the basis of the association between cultivars in mixture and monoculture, three groups of characters were distinguished. Group A characters, plant height, ear weight/tiller, grain yield/tiller, number of grains/tiller and 1000-grain weight, showed strong positive associations between performance in monoculture and mixture. Group B characters, number of tillers/plant and harvest index showed incomplete positive associations, while for group C characters, dry matter/plant, ear weight/plant, grain yield/plant and number of grains/plant, associations were weak or non-existent. Compound characters in group C showed less genetic variation in monoculture and lower general competitive effects in mixture than component characters in groups A or B. These results clearly indicate that while selection for grain yield and other characters on a per plant basis (group C characters) is confounded by intergenotypic competition, characters such as the yield components number of grains/tiller and 1000-grain weight (group A characters) are hardly affected in this range of cultivars. Selection for opposing group A characters may start in the F₂ generation, while any selection for group B and C characters should be delayed until later generations. The merits of indirect selection for yield using visual assessment of yield components are discussed. Separate analyses obtained by the inclusion of spring wheat cv. Timmo in monoculture and in the set of mixtures indicated that the use of spring wheat plants to minimise intergenotypic competition ranges from superfluous (group A characters) to useless (group C characters). A large degree of mixture advantage and the lack of complementary dominance and suppression between competitor and associate was attributed to the relatively low density of plants in the experiment which, though suitable for single plant selection, is not typical of normal seed rates for cropping.     

Evaluation of diagnostic molecular markers for DUS phenotypic assessment in the cereal crop, barley (Hordeum vulgare ssp. vulgare L.)

The deployment of genetic markers is of interest in crop assessment and breeding programmes, due to the potential savings in cost and time afforded. As part of the internationally recognised framework for the awarding of Plant Breeders’ Rights (PBR), new barley variety submissions are evaluated using a suite of morphological traits to ensure they are distinct, uniform and stable (DUS) in comparison to all previous submissions. Increasing knowledge of the genetic control of many of these traits provides the opportunity to assess the potential of deploying diagnostic/perfect genetic markers in place of phenotypic assessment. Here, we identify a suite of 25 genetic markers assaying for 14 DUS traits, and implement them using a single genotyping platform (KASPar). Using a panel of 169 UK barley varieties, we show that phenotypic state at three of these traits can be perfectly predicted by genotype. Predictive values for an additional nine traits ranged from 81 to 99?%. Finally, by comparison of varietal discrimination based on phenotype and genotype resulted in correlation of 0.72, indicating that deployment of molecular markers for varietal discrimination could be feasible in the near future. Due to the flexibility of the genotyping platform used, the genetic markers described here can be used in any number or combination, in-house or by outsourcing, allowing flexible deployment by users. These markers are likely to find application where tracking of specific alleles is required in breeding programmes, or for potential use within national assessment programmes for the awarding of PBRs.     

Accounting for competition in genetic analysis, with particular emphasis on forest genetic trials

Available experimental evidence suggests that there are genetic differences in the abilities of trees to compete for resources, in addition to non-genetic differences due to micro-site variation. The use of indirect genetic effects within the framework of linear mixed model methodology has been proposed for estimating genetic parameters and responses to selection in the presence of genetic competition. In this context, an individual’s total breeding value reflects the effects of its direct breeding value on its own phenotype and its competitive breeding value on the phenotype of its neighbours. The present study used simulated data to investigate the relevance of accounting for competitive effects at the genetic and non-genetic levels in terms of the estimation of (co)variance components and selection response. Different experimental designs that resulted in different genetic relatedness levels within a neighbourhood and survival were other key issues examined. Variances estimated for additive genetic and residual effects tended to be biased under models that ignored genetic competition. Models that fitted competition at the genetic level only also resulted in biased (co)variance estimates for direct additive, competitive additive and residual effects. The ability to detect the correct model was reduced when relatedness within a neighbourhood was very low and survival decreased. Selection responses changed considerably between selecting on breeding value estimates from a model ignoring genetic competition and total breeding estimates using the correct model. Our results suggest that considering a genetic basis to competitive ability will be important to optimise selection programmes for genetic improvement of tree species.     

Conversion of an RFLP marker for the barley stem rust resistance geneRpg1 to a specific PCR-amplifiable polymorphism

TheRpg1 gene in barley has provided satisfactory levels of stem rust resistance for the last 50 years. The appearance of a new race of stem rust that is virulent toRpg1 has resulted in efforts to incorporate new stem rust resistance genes into barley. Marker-assisted selection may provide the only means of combining this useful gene with resistance genes for which no virulent races have been identified. Several RFLP markers have been identified as linked to theRpg1 locus. One of these, ABG704 was converted into a post-amplification restriction polymorphism. To generate a specific PCR-amplifiable polymorphism the sequence of the ABG704 locus from four barley cultivars was determined. Primers were developed that can detect a single-base difference between resistant and susceptible cultivars. The successful conversion of an RFLP marker to an allele-specific PCR-based marker not only demonstrates that this type of conversion is possible for cereals, but also results in an immediately useful marker for application to plant breeding programmes.     

Allele-specific amplification of polymorphic sites for the detection of powdery mildew resistance loci in cereals

Primers for the polymerase chain reaction (PCR) were tailored to selectively amplify RFLP marker alleles associated with resistance and susceptibility for powdery mildew in cereals. The differentiation between marker alleles for susceptible and resistant genotypes is based on the discrimination of a single nucleotide by using allele-specific oligonucleotides as PCR primers. The PCR assays developed are diagnostic for RFLP alleles at the loci MWG097 in the barley genome and Whs350 in the wheat genome. The first marker locus is closely linked to MlLa resistance in barley, while the latter is linked to Pm2 resistance locus in wheat. PCR analysis of 31 barley and 30 wheat cultivars, with some exceptions, verified the presence or absence of the resistance loci investigated. These rapid PCR-based approaches are proposed as an efficient alternative to conventional procedures for selecting powdery mildew-resistant genotypes in breeding programs.     

Genotypic variation in response of barley to boron deficiency

Responses of a range of barley (Hordeum vulgare L.) genotypes to boron (B) deficiency were studied in two experiments carried out in sand culture and in the field at Chiang Mai, Thailand. In experiment 1, two barley genotypes, Stirling (two-row) and BRB 2 (six-row) and one wheat (Triticum aestivum L.) genotype, SW 41, were evaluated in sand culture with three levels of applied B (0, 0.1 and 1.0 μM B) to the nutrient solution. It was found that B deficiency depressed flag leaf B concentration at booting, grain number and grain yield of all genotypes. In barley Stirling, B deficiency also depressed number of spikes plant^-1, spikelets spike^-1 and straw yield. However, no significant difference between genotypes in flag leaf B concentration was found under low B treatments. Flag leaf B concentration below 4 mg kg^-1 was associated with grain set reduction and could, therefore, be used as a general indicator for B status in barley. In experiment 2, nine barley and two wheat genotypes were evaluated in the field on a low B soil with three levels of B. Boron levels were varied by applying either 2 t of lime ha^-1 (BL), no B (B0) or 10 kg Borax ha^-1 (B+) to the soil prior to sowing. Genotypes differed in their B response for grain spike^-1, grain spikelet^-1 and grain set index (GSI). The GSI of the B efficient wheat, Fang 60, exceeded 90% in all B treatments. The B inefficient wheat SW 41 and most of the barley genotypes set grain normally (GSI >80%) only at the B+. In B0 GSI of the barley genotypes ranged from 23% to 84%, and in BL from 19% to 65%. Three of the barley with severely depressed GSI in B0 and BL also had a decreased number of spikelets spike^-1. In experiment 3, 21 advanced barley lines from the Barley Thailand Yield Nursery 1997/98 (BTYN 1997/98) were screened for B response in sand culture with no added B. Grain Set Index of the Fang 60 and SW 41 checks were 98 and 65%, respectively, and GSI of barley lines ranged between 5 and 90%. One advanced line was identified as B efficient and two as moderately B efficient. The remaining lines ranked between moderately inefficient to inefficient. These experiments have established that there is a range of responses to B in barley genotypes. This variation in the B response was observed in vegetative as well as reproductive growth. Boron efficiency should be considered in breeding and selection of barley in low B soils. This revised version was published online in June 2006 with corrections to the Cover Date.     

Tests for the presence of gametoclonal variation in barley and wheat doubled haploids produced using the Hordeum bulbosum system

Summary To investigate whether the Hordeum bulbosum system of doubled haploid production generates gametoclonal variation, populations of second generation doubled haploid lines were developed from first generation doubled haploid lines of two barley varieties and three wheat genotypes. In barley, no variation between doubled haploids from doubled haploids was detected for a range of quantitative characters, suggesting the absence of any gametoclonal effects. However, the original selfed-seed stocks were shown to contain cryptic allelic variation for some of the characters investigated. In wheat, gametoclonal variation was detected for ear emergence time, plant height and yield, and its components for two out of the three genotypes investigated. The type and range of variation was similar to that reported from studies of somaclonal variation from immature embryos and gametoclonal variation from anther culture. Generally, the effects appeared to reduce the yield performance of individual lines. The difference in response between the two species and the consequences for the use of the doubled haploid system in breeding programmes are discussed.     

Effect of chemical forms of cadmium,zinc, and lead in polluted soils on their uptake by cabbage plants

Sorghum (Sorhum bicolor L. Moench) is an important cereal crop of the world. Performance of sorghum in acid infertile soils that are common to the tropics is rather poor. Research was undertaken in greenhouse and field conditions to evaluate the differences in growth, grain yield, and nutrient efficiency ratio (NER) of sorghum genotypes grown at three levels of Al saturation. The growth of shoots and roots and the grain yields showed significant differences with respect to Al-saturation, genotypes and their interactions. The shoot weights, root weights, and visual scores of the greenhouse study were highly related to grain yields obtained in field. The greenhouse technique adapted in this study appears to be a reliable method for separation of genotypes into Al-tolerant and intolerant types. The NER values helped differentiate genotypes into efficient and inefficient utilizers of the absorbed nutrients. The sorghum entries showed intraspecific genetic diversity in growth and NER values for the essential elements in the presence or absence of toxic levels of Al. We concluded that selection of acid soil tolerant genotypes and further breeding of acid soil (Al) tolerant cultivars is feasible in sorghum.IICA/EMBRAPA/World Bank     

Competitive interactions in Drosophila melanogaster

A competition experiment with Drosophila melanogaster is reported which comprised a replacement series with two genotypes, together with pure cultures of both genotypes at the same densities as they appeared in the mixtures. The results for total numbers and weights make clear the need to separate the intergenotypic from the intragenotypic interactions if an unambiguous interpretation of the outcome of such mixtures is to be obtained. Further experiments were carried out to investigate the behaviour of pure cultures in order to gain insight into the relative simplicity or complexity of the intragenotypic interactions that needed to be taken into account when investigating mixtures. It was found that transformation of the measurements into percent survival and average weight per fly led to relations with density which were more nearly linear than the originals and, hence, were more readily amenable to analysis. Two main points emerged from the experiments. First, the relationship between the two transformed characters did not appear straightforward. Secondly, the intragenotypic interactions, particularly for percent survival, were complex and thus provided not support for assuming them to be simple when present in mixtures of genotypes.     

A comparison of hydroponic and soil-based screening methods to identify salt tolerance in the field in barley

Success in breeding crops for yield and other quantitative traits depends on the use of methods to evaluate genotypes accurately under field conditions. Although many screening criteria have been suggested to distinguish between genotypes for their salt tolerance under controlled environmental conditions, there is a need to test these criteria in the field. In this study, the salt tolerance, ion concentrations, and accumulation of compatible solutes of genotypes of barley with a range of putative salt tolerance were investigated using three growing conditions (hydroponics, soil in pots, and natural saline field). Initially, 60 genotypes of barley were screened for their salt tolerance and uptake of Na(+), Cl(-), and K(+) at 150 mM NaCl and, based on this, a subset of 15 genotypes was selected for testing in pots and in the field. Expression of salt tolerance in saline solution culture was not a reliable indicator of the differences in salt tolerance between barley plants that were evident in saline soil-based comparisons. Significant correlations were observed in the rankings of genotypes on the basis of their grain yield production at a moderately saline field site and their relative shoot growth in pots at EC(e) 7.2 [Spearman's rank correlation (rs)=0.79] and EC(e) 15.3 (rs=0.82) and the crucial parameter of leaf Na(+) (rs=0.72) and Cl(-) (rs=0.82) concentrations at EC(e) 7.2 dS m(-1). This work has established screening procedures that correlated well with grain yield at sites with moderate levels of soil salinity. This study also showed that both salt exclusion and osmotic tolerance are involved in salt tolerance and that the relative importance of these traits may differ with the severity of the salt stress. In soil, ion exclusion tended to be more important at low to moderate levels of stress but osmotic stress became more important at higher stress levels. Salt exclusion coupled with a synthesis of organic solutes were shown to be important components of salt tolerance in the tolerant genotypes and further field tests of these plants under stress conditions will help to verify their potential utility in crop-improvement programmes.     

Recurrent selection alternating with haploid steps — a rapid breeding procedure for combining agronomic traits in inbreeders

Summary Doubled haploid lines are increasingly used in practical breeding programs. Depending on the nature of the starting material as well as on the breeding aims, one or more haploid steps are recommended, and F₁ hybrids or selfed progenies in later generations serve as starting material for the haploidization. It is demonstrated that one haploid step followed by selection in the greenhouse and in the field during the first androgenetic (A₁) and two subsequent selfed generations (A₂; A₃) is the most efficient procedure, if characters from related varieties are to be combined. For breeding programs that include wild types or unrelated genotypes, recurrent selection alternating with several haploid steps is the most efficient. A prerequisite for successful application of this combination of repeated haploidization and selection steps alternating with backcrosses is an effective selection system. The different approaches are demonstrated on a winter barley breeding program, with the central aim of combining the qualitatively inherited character resistance to barley yellow mosaic virus with quantitatively inherited complexes, particularly yield.     

Prospects for molecular breeding of barley

Data from UK Recommended List Trials showed that the introduction of new cultivars of spring and winter barley has maintained a significant increase in yield over time, whereas there has been no significant improvement in hot water extract, the major determinant of good malting quality, in either crop. Commercial barley breeding is based upon phenotypic selection, and the introduction of molecular breeding methods must either increase the rate of advance, or offer an improvement in the cost‐effectiveness of breeding programmes. Molecular breeding can be applied to either single gene or polygenic characters but is not widely used in commercial barley breeding, other than as a marker for resistance to the Barley Yellow Mosaic Virus complex. There are many reports of potential targets for use in molecular breeding but the few validation studies that have been carried out to date are disappointing. Results from genomics studies are likely to lead to the identification of key candidate genes, which can be associated with economically important characters through co‐location on certain chromosomal regions. Associations between candidate gene sequence haplotypes and phenotypic characteristics is expected to identify allelic combinations, which are most frequently observed in successful cultivars, that can be used in molecular breeding of barley on a commercial scale.     

Rapid upregulation ofDehyrin3 andDehydrin4 in response to dehydration is a characteristic of drought-tolerant genotypes in barley

The identification of molecular markers and marker-aided selection are essential to the efficient breeding of drought-tolerant plants. However, because that characteristic is controlled by many quantitative trait loci, such markers that can screen and trace desirable barley genotypes in a segregating population or germplasm have not yet been determined. Relative water content has been used to estimate drought tolerance in plants because it is highly correlated with the drought index of yield. To develop reliable gene-specific markers for identifying tolerant versus susceptible genotypes, we performed suppression subtractive hybridization to identify candidate genes. We used two domestic barley cultivars, one having the highest RWC (drought-tolerant ‘Chalbori’) and the other having the lowest (drought-susceptible ‘Daebaekbori’). In response to dehydration at the early seedling stage, rapid upregulation ofDehydrin3 (Dhn3) andDhn4 occurred in the drought-tolerant genotypes, but not in the susceptible ones. Similar results were obtained with mature plants growing under frequent drought stress in the greenhouse. In addition,Dhn3 andDhn4 conferred higher drought tolerance when they were over-expressed in transgenicArabidopsis. Thus, in addition to using assessments of RWC, we propose thatDhn3 andDhn4 expressions can serve as drought-induced gene-specific markers to determine drought-tolerant barley genotypes at the seedling stage.     

Hybridization and selection for improving seed protein in barley

Summary Hybridization followed by continuous selection of lines of barley from different cross-combinations involving high protein-high lysine genotypes and the agronomically superior strains resulted in breaking the negative correlations between 1000 grain weight and high protein content and high DBC values. The methodology of DBC-Kjeldahl protein adopted in the present study is likely to be useful in identifying high lysine lines. The present study has shown considerable variability with respect to protein content and grain weight and has provided interesting genotypes which can be used in synthesising lines with improved nutritional quality and productivity in barley. The success in breaking the undesirable linkages to factors that impair the endosperm development is due to sufficient genetic variability in the initial breeding material as well as the use of suitable breeding procedures like the full-sib mating in the early segregating generations.     

Soil aluminium effects on uptake,influx, and transport of nutrients in sorghum genotypes

Sorghum [Sorghum bicolor (L.) Moench] is the fifth most important cereal crop of the world. In South America, it is grown mainly on acid soils, and its production on these soils is limited by deficient levels of available P, Ca, Mg, and micronutrients, and toxic levels of Al and Mn. A greenhouse experiment was undertaken to evaluate the genotypic differences in sorghum for uptake (U), inhibition (IH), influx (IN) into roots, and transport (TR) to shoot for nutrients at three levels of soil Al saturation (2, 41, 64%). Overall shoot nutrient U, IN, and TR showed a significant inverse correlation with soil Al saturation and shoot Al concentration, and a significant positive correlation with shoot and root dry weight. The nutrient uptake parameters differentiated genotypes into most and least efficient categories at various levels of soil Al saturation. The nutrient uptake parameters showed significant differences with respect to soil Al saturation, genotypes, and their interactions. In the current study, Al tolerant genotypes recorded higher IN and TR for P, K, Ca, Mg, Zn, and Fe than Al-sensitive genotypes. Therefore, these U, IN, and TR traits could be used in selection of sorghum plants adaptable to acid soils. Sorghum genotypes used in this study showed intraspecific genetic diversity in U, IN, and TR for essential nutrients. It was concluded that selection of acid soil tolerant genotypes and further breeding of acid (Al) tolerant sorghum cultivars are feasible.IICA/EMBRAPA/World BankIICA/EMBRAPA/World BankIICA/EMBRAPA/World Bank     

RAPD markers linked to the Vf gene for scab resistance in apple

Scab (Venturia inaequalis) is one of the most harmful diseases of apple, significantly affecting world apple production. The identification and early selection of resistant genotypes by molecular markers would greatly improve breeding strategies. Bulked segregant analysis was chosen for the identification of RAPD markers linked to the Vf scab resistant gene. Five different RAPD markers, derived from the wild species Malus floribunda. 821, were identified, and their genetic distance from Vf gene was estimated. The markers OPAM19₂₂₀₀ and OPAL07₅₈₀ were found to be very closely linked to the Vf gene. This result was indirectly confirmed by the analysis of resistant genotypes collected from various breeding programmes. Except for cv Murray, which carries the Vm gene, all these resistant genotypes showed the markers OPAM19₂₂₀₀ and OPAL07₅₈₀.     

Integrated genomic selection for rapid improvement of crops

An increase in the rate of crop improvement is essential for achieving sustained food production and other needs of ever-increasing population. Genomic selection (GS) is a potential breeding tool that has been successfully employed in animal breeding and is being incorporated into plant breeding. GS promises accelerated breeding cycles through a rapid selection of superior genotypes. Numerous empirical and simulation studies on GS and realized impacts on improvement in the crop yields are recently being reported. For a holistic understanding of the technology, we briefly discuss the concept of genetic gain, GS methodology, its current status, advantages of GS over other breeding methods, prediction models, and the factors controlling prediction accuracy in GS. Also, integration of speed breeding and other novel technologies viz. high throughput genotyping and phenotyping technologies for enhancing the efficiency and pace of GS, followed by its prospective applications in varietal development programs is reviewed.     

Development of YLM, a codominant PCR marker closely linked to the Yd2 gene for resistance to barley yellow dwarf disease

 The Yd2 gene in barley provides protection against barley yellow dwarf luteovirus (BYDV), the most economically devastating virus of cereals worldwide. Because resistance assays to identify Yd2-containing individuals from breeding populations are often difficult, we have developed a closely linked, codominant PCR-based marker for Yd2 using AFLP marker technology. The marker, designated YLM, can be amplified from barley genomic DNA prepared using a rapid and simple extraction procedure and, in a survey of more than 100 barley genotypes, was found to be polymorphic between most Yd2 and non-Yd2 lines. The YLM therefore shows excellent potential as a tool for selecting Yd2-carrying segregants in barley breeding programmes. Received: 15 August 1997 / Accepted: 1 December 1997     

Effect of yellow rust on yield components of barley cultivars with race-specific and slow rusting resistance to yellow rust

Yellow rust caused by Puccinia striiformis f. sp. hordei is an important disease of barley (Hordeum vulgare L.) in some parts of the world. We compared the effectiveness of different types of resistance in field plots at Ardabil Agricultural Research Station (Iran) during 2010–2011. Yield components along with slow rusting parameters including final rust severity (FRS), apparent infection rate (r), relative area under disease progress curve (rAUDPC) and coefficient of infection (CI) were evaluated for 25 barley cultivars. In all, two barley cultivars with race-specific resistance, 19 cultivars with different levels of slow rusting resistance and four susceptible cultivars were included in two experiments with and without fungicide protection under high disease pressure. Barley cultivars with slow rusting resistance displayed a range of severity responses indicating phenotypic diversity. Mean thousand kernels weight (TKW) losses for susceptible, race-specific and slow rusting genotypes were 31, 3 and 12%, respectively, and mean kernels per spike (KPS) losses for susceptible, race-specific and slow rusting genotypes were 19, 0.2 and 8%, respectively. Correlation coefficient of mean TKW and KPS losses with epidemiological parameters; rAUDPC, r, CI and FRS were highly significant. Slow rusting cultivars with low values of different parameters as well as genotypes with low yield component losses despite moderate disease levels were identified. Such genotypes can be used for breeding barely genotypes with high levels of resistance and negligible yield losses.