AFLP-based assessment of genetic diversity among nine alfalfa germplasms using bulk DNA templates

Genetic variations in Turkey cultivar and ecotype Medicago sativa species: cytological, total protein profile, and molecular characterization

BACKGROUND

Alfalfa (Medicago sativa L.) is a perennial plant, which is high in nutritional value and resistant to environmental conditions, and it is one of most frequently preferred feed crop among the leguminous family. In this study, it was aimed to determine the genetic diversity of some alfalfa ecotypes and their varieties by DNA, protein, nucleus, and chromosome counts. The genetic distance between the populations of control (M. truncatula), five different cultivars (Alsancak, Bilensoy, Iside, Plato, Bilensoy82), and three different ecotypes (Erzurum, Muş, and Konya) was investigated by cytogenetic analysis, flow cytometry, simple sequence repeats (SSR), and SDS PAGE techniques.

RESULTS

Cytogenetic analysis of these tested plants has verified the existence of expected levels such as diploid, triploid, and tetraploid as well as aneuploid (2n = 4x = 30) plants. Flow cytometry analysis have displayed that all of tested plants were tetraploid, whereas cytological analysis had either diploid, triploid, or tetraploid. Genetic diversity dendrogram was created using Erzurum, Muş, Konya, Bilensoy82, Alsancak, and Plato varieties. The Iside and Bilensoy were found to be morphogenetic in relationship. Our control plant, M. truncatula, did not have a similarity relationship with other ecotypes and cultivars. The total numbers of protein bands differed among tested plants from 140 kDA to 25 kDa.

CONCLUSIONS

This paper first reports on the genetic variation of Turkish alfalfa plants by using detailed analysis techniques. This work provides important findings for the classification, conservation, and innovation of alfalfa germplasm resources.

Genetic diversity of maize landraces from the South-West of France

From the 17th century until the arrival of hybrids in 1960s, maize landraces were cultivated in the South-West of France (SWF), a traditional region for maize cultivation. A set of landraces were collected in this area between the 1950s and 1980s and were then conserved ex situ in a germplam collection. Previous studies using molecular markers on approx. twenty landraces from this region suggested that they belonged to a Pyrenees-Galicia Flint genetic group and originated from hybridizations between Caribbean and Northern Flint germplasms introduced to Europe. In this study, we assessed the structure and genetic diversity of 194 SWF maize landraces to better elucidate their origin, using a 50K SNP array and a bulk DNA approach. We identified two weakly differentiated genetic groups, one in the Western part and the other in the Eastern part of the studied region. We highlighted the existence of a longitudinal gradient along the SWF area that was probably maintained through the interplay between genetic drifts and restricted gene flows. The contact zone between the two groups observed near the Garonne valley may be the result of these evolutionnary forces. We found in landraces from the East part of the region significant cases of admixture between landraces from the Northern Flint group and landraces from either the Caribbean, Andean or Italian groups. We then assumed that SWF landraces had a multiple origin with a predonderance of Northern Flint germplasm for the two SWF groups, notably for the East part.

Deciphering the Genetic Diversity of Landraces With High-Throughput SNP Genotyping of DNA Bulks: Methodology and Application to the Maize 50k Array

Genebanks harbor original landraces carrying many original favorable alleles for mitigating biotic and abiotic stresses. Their genetic diversity remains, however, poorly characterized due to their large within genetic diversity. We developed a high-throughput, cheap and labor saving DNA bulk approach based on single-nucleotide polymorphism (SNP) Illumina Infinium HD array to genotype landraces. Samples were gathered for each landrace by mixing equal weights from young leaves, from which DNA was extracted. We then estimated allelic frequencies in each DNA bulk based on fluorescent intensity ratio (FIR) between two alleles at each SNP using a two step-approach. We first tested either whether the DNA bulk was monomorphic or polymorphic according to the two FIR distributions of individuals homozygous for allele A or B, respectively. If the DNA bulk was polymorphic, we estimated its allelic frequency by using a predictive equation calibrated on FIR from DNA bulks with known allelic frequencies. Our approach: (i) gives accurate allelic frequency estimations that are highly reproducible across laboratories, (ii) protects against false detection of allele fixation within landraces. We estimated allelic frequencies of 23,412 SNPs in 156 landraces representing American and European maize diversity. Modified Roger's genetic Distance between 156 landraces estimated from 23,412 SNPs and 17 simple sequence repeats using the same DNA bulks were highly correlated, suggesting that the ascertainment bias is low. Our approach is affordable, easy to implement and does not require specific bioinformatics support and laboratory equipment, and therefore should be highly relevant for large-scale characterization of genebanks for a wide range of species.

Identification of Single-Nucleotide Polymorphic Loci Associated with Biomass Yield under Water Deficit in Alfalfa (Medicago sativa L.) Using Genome-Wide Sequencing and Association Mapping

Alfalfa is a worldwide grown forage crop and is important due to its high biomass production and nutritional value. However, the production of alfalfa is challenged by adverse environmental factors such as drought and other stresses. Developing drought resistance alfalfa is an important breeding target for enhancing alfalfa productivity in arid and semi-arid regions. In the present study, we used genotyping-by-sequencing and genome-wide association to identify marker loci associated with biomass yield under drought in the field in a panel of diverse germplasm of alfalfa. A total of 28 markers at 22 genetic loci were associated with yield under water deficit, whereas only four markers associated with the same trait under well-watered condition. Comparisons of marker-trait associations between water deficit and well-watered conditions showed non-similarity except one. Most of the markers were identical across harvest periods within the treatment, although different levels of significance were found among the three harvests. The loci associated with biomass yield under water deficit located throughout all chromosomes in the alfalfa genome agreed with previous reports. Our results suggest that biomass yield under drought is a complex quantitative trait with polygenic inheritance and may involve a different mechanism compared to that of non-stress. BLAST searches of the flanking sequences of the associated loci against DNA databases revealed several stress-responsive genes linked to the drought resistance loci, including leucine-rich repeat receptor-like kinase, B3 DNA-binding domain protein, translation initiation factor IF2, and phospholipase-like protein. With further investigation, those markers closely linked to drought resistance can be used for MAS to accelerate the development of new alfalfa cultivars with improved resistance to drought and other abiotic stresses.

AFLP assessment of genetic variability and relationships in an Asian wild germplasm collection of Dactylis glomerata L

Orchardgrass (Dactylis glomerata L.), an excellent perennial and cool season forage species distributed in most temperate regions, has been cultivated widely in Western China. Amplified fragment length polymorphism markers were employed to determine the genetic variability and population structure among 41 indigenous orchardgrass accessions from Central Asia and Western China. On the basis of 531 polymorphic fragments resulted from eight primer combinations, polymorphic information content (PIC), marker index (MI) and resolving power (RP) averaged 0.252, 16.34 and 25.27 per primer combination, respectively, demonstrating the high efficiency and reliability of the markers used. We found relatively low differentiation (Fst=0.135) for three geographical groups, where Central Asia (CA) and Southwest China (SWC) group exhibited higher intra-population diversity (He=0.20 and 0.21) than that of the Xinjiang (XJ) group (He=0.14). We also did not detect a clear pattern of isolation by distance with a low value of r=0.301 in the Mantel test. STRUCTURE, FLOCK, UPGMA clustering and PCoA analyses showed that CA group is more related to the SWC Group rather than to the XJ Group. In addition, this study strongly suggests that geographical and ecological environmental factors together could better explain the genetic differentiation between different geographical regions than geographic isolation alone, especially for Xinjiang accessions. The present study also could support that Southwest China might be the internal diversity center of D. glomerata in China. The knowledge about the genetic variability of the Asian accessions examined contributes to rapid characterization, defining gene pools of wild accessions, and selecting appropriate germplasms for plant improvement.

Transcript analysis in two alfalfa salt tolerance selected breeding populations relative to a non-tolerant population

With the growing limitations on arable land, alfalfa (a widely cultivated, low-input forage) is now being selected to extend cultivation into saline lands for low-cost biofeedstock purposes. Here, minerals and transcriptome profiles were compared between two new salinity-tolerant North American alfalfa breeding populations and a more salinity-sensitive western Canadian alfalfa population grown under hydroponic saline conditions. All three populations accumulated two-fold higher sodium in roots than shoots as a function of increased electrical conductivity. At least 50% of differentially expressed genes (p < 0.05) were down-regulated in the salt-sensitive population growing under high salinity, while expression remained unchanged in the saline-tolerant populations. In particular, most reduction in transcript levels in the salt-sensitive population was observed in genes specifying cell wall structural components, lipids, secondary metabolism, auxin and ethylene hormones, development, transport, signalling, heat shock, proteolysis, pathogenesis-response, abiotic stress, RNA processing, and protein metabolism. Transcript diversity for transcription factors, protein modification, and protein degradation genes was also more strongly affected in salt-tolerant CW064027 than in salt-tolerant Bridgeview and salt-sensitive Rangelander, while both saline-tolerant populations showed more substantial up-regulation in redox-related genes and B-ZIP transcripts. The report highlights the first use of bulked genotypes as replicated samples to compare the transcriptomes of obligate out-cross breeding populations in alfalfa.

Identification of Loci Associated with Drought Resistance Traits in Heterozygous Autotetraploid Alfalfa (Medicago sativa L.) Using Genome-Wide Association Studies with Genotyping by Sequencing

Drought resistance is an important breeding target for enhancing alfalfa productivity in arid and semi-arid regions. Identification of genes involved in drought tolerance will facilitate breeding for improving drought resistance and water use efficiency in alfalfa. Our objective was to use a diversity panel of alfalfa accessions comprised of 198 cultivars and landraces to identify genes involved in drought tolerance. The panel was selected from the USDA-ARS National Plant Germplasm System alfalfa collection and genotyped using genotyping by sequencing. A greenhouse procedure was used for phenotyping two important traits associated with drought tolerance: drought resistance index (DRI) and relative leaf water content (RWC). Marker-trait association identified nineteen and fifteen loci associated with DRI and RWC, respectively. Alignments of target sequences flanking to the resistance loci against the reference genome of M. truncatula revealed multiple chromosomal locations. Markers associated with DRI are located on all chromosomes while markers associated with RWC are located on chromosomes 1, 2, 3, 4, 5, 6 and 7. Co-localizations of significant markers between DRI and RWC were found on chromosomes 3, 5 and 7. Most loci associated with DRI in this work overlap with the reported QTLs associated with biomass under drought in alfalfa. Additional significant markers were targeted to several contigs with unknown chromosomal locations. BLAST search using their flanking sequences revealed homology to several annotated genes with functions in stress tolerance. With further validation, these markers may be used for marker-assisted breeding new alfalfa varieties with drought resistance and enhanced water use efficiency.

Genetic variation and relationship of alfalfa populations and their progenies based on RAPD markers

The aim of investigation was to evaluate genetic variation and relationship among alfalfa populations and their offspring, with minimal cost, by using DNA marker analysis. RAPD analysis was performed on bulked DNA samples of five alfalfa parental populations and their progenies: 20 F1 populations from reciprocal diallel crosses and five S1 populations from self-pollination. Twenty primers generated 217 bands, ranging in size from 300 to 6000 bp, with the average number of bands per primer of 10.85 and polymorphism information content of 0.246. Percentage of polymorphic loci, effective number of alleles, expected heterozygosity and Shannon’s information index were used to estimate genetic variation. Higher diversity was observed in F1 progeny populations, while genetic variation in parental populations and S1 progenies remained similar. The genetic relatedness of alfalfa populations was analysed by UPGMA and Bayesian model-based clustering approach. In both types of analysis selfpollinated progenies were grouped. Furthermore, the hybrid offspring where Zuzana, and RSI 20 were maternal parents were placed in separate groups. The results indicate that use of RAPD markers on bulked DNA samples can be fast and cost-effective way for differentiation of alfalfa parental populations and their offspring, as well as for evaluation of their genetic relationships.

Analysis and optimization of bulk DNA sampling with binary scoring for germplasm characterization

The strategy of bulk DNA sampling has been a valuable method for studying large numbers of individuals through genetic markers. The application of this strategy for discrimination among germplasm sources was analyzed through information theory, considering the case of polymorphic alleles scored binarily for their presence or absence in DNA pools. We defined the informativeness of a set of marker loci in bulks as the mutual information between genotype and population identity, composed by two terms: diversity and noise. The first term is the entropy of bulk genotypes, whereas the noise term is measured through the conditional entropy of bulk genotypes given germplasm sources. Thus, optimizing marker information implies increasing diversity and reducing noise. Simple formulas were devised to estimate marker information per allele from a set of estimated allele frequencies across populations. As an example, they allowed optimization of bulk size for SSR genotyping in maize, from allele frequencies estimated in a sample of 56 maize populations. It was found that a sample of 30 plants from a random mating population is adequate for maize germplasm SSR characterization. We analyzed the use of divided bulks to overcome the allele dilution problem in DNA pools, and concluded that samples of 30 plants divided into three bulks of 10 plants are efficient to characterize maize germplasm sources through SSR with a good control of the dilution problem. We estimated the informativeness of 30 SSR loci from the estimated allele frequencies in maize populations, and found a wide variation of marker informativeness, which positively correlated with the number of alleles per locus.

RAPD polymorphism in the prebreeding material for cultivation of synthetic variations of lucerne (Medicago sativa L.)

Genetic diversity between synthetic cultivars (Syn5, Syn7), inbred lines (D3, D5, E1/2, G1/1, G1/2) and ecotypes (E16, E51, E182, E231) of lucerne (Medicago sativa L.) was studied using the RAPD-PCR method. The plants differed in the efficiency of seed set and in the yield of green mass. The ecotypes E182 and E231 and the synthetic population Syn5 showed the highest fertility. Additionally, Syn5 also showed the highest efficiency of seed set and the yield of green mass. Among the inbred lines, D3 was characterised by the highest yield of green mass and E1/2 by the highest fertility. An optimal combination of yield and biomass was observed for the synthetic population Syn5, obtained by crossing the lines D3, D5 and G1/1, as demonstrated using comparative analysis. A total of 338 polymorphic products were generated using 20 arbitrary primers. Cluster analysis using the Unweighted-Pair Group Method with Arithmetic Mean (UPGMA) in the Molecular image Gel Doc™ XR (Bio-Rad) software based on the Dice’s coefficient of genetic similarity showed a division of the studied forms into two groups based on genetic similarity. The ecotype E16 formed one of the groups whereas all of the other ecotypes observed in this study clustered into the second group. A high level of polymorphism among the studied lucerne forms was detected indicating an interesting gene pool awaiting future exploration. Analysis of variance also supported a high diversity among the studied forms. This study provides insightful information into the heterosis effect of synthetic populations or hybrids of F1 lucerine by providing correlations between the genetic background of the inbred lines and their ability to produce a specific yield.

System responses to long-term drought and re-watering of two contrasting alfalfa varieties

Systems analysis of two alfalfa varieties, Wisfal (Medicago sativa ssp. falcata var. Wisfal) and Chilean (M. sativa ssp. sativa var. Chilean), with contrasting tolerance/sensitivity to drought revealed common and divergent responses to drought stress. At a qualitative level, molecular, biochemical, and physiological responses to drought stress were similar in the two varieties, indicating that they employ the same strategies to cope with drought. However, quantitative differences in responses at all levels were revealed that may contribute to greater drought tolerance in Wisfal. These included lower stomatal density and conductance in Wisfal; delayed leaf senescence compared with Chilean; greater root growth following a drought episode, and greater accumulation of osmolytes, including raffinose and galactinol, and flavonoid antioxidants in roots and/or shoots of Wisfal. Genes encoding transcription factors and other regulatory proteins, and genes involved in the biosynthesis of osmolytes and (iso)flavonoids were differentially regulated between the two varieties and represent potential targets for improving drought tolerance in alfalfa in the future.

Complex patterns of autopolyploid evolution in alfalfa and allies (Medicago sativa; Leguminosae)

PREMISE OF THE STUDY

Although there is growing evidence that autopolyploidy is a widespread and important evolutionary phenomenon, it has received less attention than allopolyploidy. Medicago sativa comprises several diploid and autopolyploid taxa, including autotetraploid cultivated alfalfa, and affords an opportunity to elucidate the evolutionary history of a morphologically and genetically complex autopolyploid system.

METHODS

Phylogenies and haplotype networks were constructed from two chloroplast noncoding regions (rpl20-rps12 and trnS-trnG spacers) across seven diploid and polyploid infraspecific taxa of M. sativa and five additional closely related Medicago species, and genetic differentiation was estimated.

KEY RESULTS

The two most prominent M. sativa autopolyploids have contrasting evolutionary histories. Chloroplast data support a simple autopolyploid origin of subsp. sativa (alfalfa) from diploid subsp. caerulea, from which it is distinguishable in several quantitative characters. In contrast, morphologically identical diploid and autopolyploid cytotypes of subsp. falcata were found to possess very different chloroplast haplotypes, suggesting past introgression from M. prostrata into the polyploid. Despite the presence of hybrids between tetraploid subspecies falcata and sativa, there was little evidence of introgression of chloroplast genomes from either subspecies into the other.

CONCLUSIONS

Autopolyploid evolution in M. sativa is complicated and has followed very different paths in different subspecific taxa. The potential exists for gene flow in virtually all combinations of subspecies both within and between ploidies, yet despite the existence of hybrids, morphologically and genetically distinctive subspecies persist.

Towards an optimal sampling strategy for assessing genetic variation within and among white clover (Trifolium repens L.) cultivars using AFLP

Cost reduction in plant breeding and conservation programs depends largely on correctly defining the minimal sample size required for the trustworthy assessment of intra- and inter-cultivar genetic variation. White clover, an important pasture legume, was chosen for studying this aspect. In clonal plants, such as the aforementioned, an appropriate sampling scheme eliminates the redundant analysis of identical genotypes. The aim was to define an optimal sampling strategy, i.e., the minimum sample size and appropriate sampling scheme for white clover cultivars, by using AFLP data (283 loci) from three popular types. A grid-based sampling scheme, with an interplant distance of at least 40 cm, was sufficient to avoid any excess in replicates. Simulations revealed that the number of samples substantially influenced genetic diversity parameters. When using less than 15 per cultivar, the expected heterozygosity (He) and Shannon diversity index (I) were greatly underestimated, whereas with 20, more than 95% of total intra-cultivar genetic variation was covered. Based on AMOVA, a 20-cultivar sample was apparently sufficient to accurately quantify individual genetic structuring. The recommended sampling strategy facilitates the efficient characterization of diversity in white clover, for both conservation and exploitation.

Inferring population structure and genetic diversity of broad range of wild diploid alfalfa (Medicago sativa L.) accessions using SSR markers

Diversity analyses in alfalfa have mainly evaluated genetic relationships of cultivated germplasm, with little known about variation in diploid germplasm in the M. sativa-falcata complex. A collection of 374 individual genotypes derived from 120 unimproved diploid accessions from the National Plant Germplasm System, including M. sativa subsp. caerulea, falcata, and hemicycla, were evaluated with 89 polymorphic SSR loci in order to estimate genetic diversity, infer the genetic bases of current morphology-based taxonomy, and determine population structure. Diploid alfalfa is highly variable. A model-based clustering analysis of the genomic data identified two clearly discrete subpopulations, corresponding to the morphologically defined subspecies falcata and caerulea, with evidence of the hybrid nature of the subspecies hemicycla based on genome composition. Two distinct subpopulations exist within each subsp. caerulea and subsp. falcata. The distinction of caerulea was based on geographical distribution. The two falcata groups were separated based on ecogeography. The results show that taxonomic relationships based on morphology are reflected in the genetic marker data with some exceptions, and that clear distinctions among subspecies are evident at the diploid level. This research provides a baseline from which to systematically evaluate variability in tetraploid alfalfa and serves as a starting point for exploring diploid alfalfa for genetic and breeding experiments.

Genetic diversity analysis in blackgram (Vigna mungo (L.) Hepper) using AFLP and transferable microsatellite markers from azuki bean (Vigna angularis (Willd.) Ohwi & Ohashi)

Genetic diversity in 20 elite blackgram (Vigna mungo (L.) Hepper) genotypes was studied using microsatellite and AFLP markers. Thirty-six microsatellite markers from azuki bean (Vigna angularis (Willd.) Ohwi & Ohashi) were successfully amplified across the 20 blackgram genotypes and 33 microsatellite markers showed polymorphism. A total of 137 microsatellite alleles were generated with an average of 4.1 alleles per locus. The number of alleles ranged from two to nine and the polymorphic information content value for the microsatellite markers varied from 0.10 to 0.87 with an average of 0.49. Microsatellite markers were highly informative and a combination of only three microsatellite markers (CEDG264, CEDG173, and CEDG044) was sufficient to discriminate all 20 blackgram genotypes. In the case of AFLP, 11 primer pairs generated 324 polymorphic marker fragments. The polymorphic information content values for AFLP primer combinations ranged from 0.21 to 0.34 with an average of 0.29. Similarity measures and clustering analyses were made using microsatellite and AFLP data separately. The resulting dendrograms distributed the 20 blackgram genotypes into five main clusters. The dendrograms were comparable with each other with the Mantel test between the cophenetic matrices of microsatellite data and AFLP data showing moderate correlation (r = 0.64). The results of the principal components analysis were well congruent with the dendrograms. In the dendrograms as well as in the principal components analyses, genotype Trombay wild (Vigna mungo var. silvestris) was placed separately from rest of the genotypes. This study demonstrated that the azuki bean microsatellite markers are highly polymorphic and informative and can be successfully used for genome analysis in blackgram. Results indicate that sufficient variability is present in the blackgram genotypes and would be helpful in the selection of suitable parents for breeding purposes and gene mapping studies.

Optimization of bulked AFLP analysis and its application for exploring diversity of natural and cultivated populations of red clover

Landraces and wild populations of red clover (Trifolium pratense L.) may represent a significant yet poorly characterized genetic resource of temperate grasslands. A bulking strategy with amplified fragment length polymorphism (AFLP) markers was optimized to characterize 120 red clover populations in 6 different groups: Swiss wild clover populations, Mattenklee landraces, Mattenklee cultivars, field clover cultivars, Dutch wild clover populations, and Dutch landraces. Analysis of 2 bulked samples/population consisting of 20 plants each with12 AFLP primer combinations was found optimal for determining genetic diversity and relationships within and among red clover populations and groups. Swiss wild clover populations were clearly separated from all other red clover groups and variability within and among populations was shown to be particularly high in wild clover populations and Mattenklee landraces, emphasising their value as genetic resources for improvement of red clover cultivars, as well as for conservation and restoration of biodiversity. This study shows that the ancestry of red clover landraces is primarily found in introduced cultivars rather than in natural wild clover populations. In addition, the methodological considerations presented here may help improve diversity analyses using bulked samples.

Genetic relationship and diversity in a sesame (Sesamum indicum L.) germplasm collection using amplified fragment length polymorphism (AFLP)

Background

Sesame is an important oil crop in tropical and subtropical areas. Despite its nutritional value and historic and cultural importance, the research on sesame has been scarce, particularly as far as its genetic diversity is concerned. The aims of the present study were to clarify genetic relationships among 32 sesame accessions from the Venezuelan Germplasm Collection, which represents genotypes from five diversity centres (India, Africa, China-Korea-Japan, Central Asia and Western Asia), and to determine the association between geographical origin and genetic diversity using amplified fragment length polymorphism (AFLP).

Results

Large genetic variability was found within the germplasm collection. A total of 457 AFLP markers were recorded, 93 % of them being polymorphic. The Jaccard similarity coefficient ranged from 0.38 to 0.85 between pairs of accessions. The UPGMA dendrogram grouped 25 of 32 accessions in two robust clusters, but it has not revealed any association between genotype and geographical origin. Indian, African and Chinese-Korean-Japanese accessions were distributed throughout the dendrogram. A similar pattern was obtained using principal coordinates analysis. Genetic diversity studies considering five groups of accessions according to the geographic origin detected that only 20 % of the total diversity was due to diversity among groups using Nei's coefficient of population differentiation. Similarly, only 5% of the total diversity was attributed to differences among groups by the analysis of molecular variance (AMOVA). This small but significant difference was explained by the fact that the Central Asia group had a lower genetic variation than the other diversity centres studied.

Conclusion

We found that our sesame collection was genetically very variable and did not show an association between geographical origin and AFLP patterns. This result suggests that there was considerable gene flow among diversity centres. Future germplasm collection strategies should focus on sampling a large number of plants. Covering many diversity centres is less important because each centre represents a major part of the total diversity in sesame, Central Asia centre being the only exception. The same recommendation holds for the choice of parents for segregant populations used in breeding projects. The traditional assumption that selecting genotypes of different geographical origin will maximize the diversity available to a breeding project does not hold in sesame.

Use of AFLP Markers in Surveys of Plant Diversity

The collection of the available range of genetic variation in a gene pool, usually made of the cultivated species and their undomesticated relatives, is referred to as a germplasm collection. Increasingly, discriminator data generated using molecular genetic markers are either complementing or completely replacing those from morphological characters (known as descriptors) in surveys of genetic diversity. In addition to highlighting the state of knowledge on the specific applications of amplified fragment length polymorphisms (AFLPs) in surveys of plant genetic diversity, an attempt at a brief description and comparison of the different marker systems in use has also been made in this chapter. We have also attempted a description of the AFLP marker technology, its strengths and weaknesses, methodologies for generating reliable AFLP data, available resources (hardware, software, consumables); the kinds of questions for which AFLP data provide valid answers; and data management options. This chapter also highlights salient considerations that would guide decisions on the adoption of molecular marker assays.

Potential to increase yield in lucerne (Medicago sativa subsp. sativa) through introgression of Medicago sativa subsp. falcata into Australian adapted material

The effect of interspecific heterosis in crosses between Medicago sativa subsp. sativa and M. sativa subsp. falcata was assessed. Three sativa and 3 falcata plants were crossed in a diallel design. Progeny dry matter yield and natural plant height were assessed in a replicated field experiment at Gatton, Queensland. Yield data were analysed using the method of residual maximum likelihood (REML) and Griffing’s model 1. There were significant differences between the reciprocal, general combining ability (GCA), and specific combining ability (SCA) effects. As expected, S1 populations were lower yielding than their respective intraspecific cross and falcata × falcata crosses were significantly lower yielding than sativa × sativa crosses. Some of the interspecific crosses indicated substantial SCA effects, yielding at least as well as the best sativa × sativa crosses. We have demonstrated the potential usefulness of unselected M. sativa subsp. falcata as a heterotic group in the improvement of yield in northern Australian adapted lucerne material, and discuss how it could be incorporated into future breeding to overcome the yield stagnation currently being experienced in Australian programs.

Population-based diallel analyses among nine historically recognized alfalfa germplasms

Identification of heterotic groups and patterns among breeding populations provides fundamental information to help plant breeders more knowledgeably manipulate heterosis. A diallel analysis was conducted among nine alfalfa ( Medicago sativa L.) germplasms, commonly referred to as African, Chilean, Flemish, Indian, Ladak, M. falcata, M. varia, Peruvian, and Turkistan, which represent a significant proportion of the genetic diversity present in US cultivars. Heterotic responses were determined by evaluating forage yield of the germplasms and their 36 half-diallel hybrids in seeded plots that were harvested five times in each of 2 years. Commercially acceptable yields were obtained from some hybrids of unimproved parents, where at least one parent was adapted to the study environment. Variation among crosses was attributed primarily to general combining ability (GCA) effects; however, specific combining ability effects were also significant. GCA estimates for African, Chilean and Peruvian were positive, while those for Ladak, M. falcata, and M. varia were negative. Estimates for variety heterosis effects were positive for Peruvian and M. falcata and negative for Indian and M. varia. Significant mid-parent heterosis [(MPH) range of -21% to 55%] and high-parent heterosis [(HPH) range of -33% to 23%] was detected. M. falcata hybrids exhibited the highest MPH values. However, this likely reflects the poor yield of M. falcata per se in the study environment and consequently, low MPH values. Peruvian hybrids demonstrated the highest cross mean performance, significant positive MPH in all crosses, and positive HPH in five out of eight crosses. The results indicate that Peruvian should be recognized as a heterotic group. Alfalfa breeders may wish to explore opportunities for heterotic yield gains that are likely to exist in hybrids between the Peruvian germplasm and elite breeding populations, in particular, those adapted to the southwestern United States. MPH results suggest that alfalfa breeders may have capitalized on the heterotic response between Flemish and M. varia during past development of alfalfa synthetics adapted to the central and northern latitudes of the United States.

How to track and assess genotyping errors in population genetics studies

Genotyping errors occur when the genotype determined after molecular analysis does not correspond to the real genotype of the individual under consideration. Virtually every genetic data set includes some erroneous genotypes, but genotyping errors remain a taboo subject in population genetics, even though they might greatly bias the final conclusions, especially for studies based on individual identification. Here, we consider four case studies representing a large variety of population genetics investigations differing in their sampling strategies (noninvasive or traditional), in the type of organism studied (plant or animal) and the molecular markers used [microsatellites or amplified fragment length polymorphisms (AFLPs)]. In these data sets, the estimated genotyping error rate ranges from 0.8% for microsatellite loci from bear tissues to 2.6% for AFLP loci from dwarf birch leaves. Main sources of errors were allelic dropouts for microsatellites and differences in peak intensities for AFLPs, but in both cases human factors were non-negligible error generators. Therefore, tracking genotyping errors and identifying their causes are necessary to clean up the data sets and validate the final results according to the precision required. In addition, we propose the outline of a protocol designed to limit and quantify genotyping errors at each step of the genotyping process. In particular, we recommend (i) several efficient precautions to prevent contaminations and technical artefacts; (ii) systematic use of blind samples and automation; (iii) experience and rigor for laboratory work and scoring; and (iv) systematic reporting of the error rate in population genetics studies.