Multiallelic Markers Research Articles

Association Mapping of Thousand Grain Weight using SSR and SNP Markers in Rice (Oryza sativa L.) Across Six Environments

Thousand grain weight (TGW) is an important determinant of rice yield, and correlates with grain size, plumpness and grain number per panicle. In rice, there are fewer association mapping studies relating grain weight traits using both SSR and SNP markers. In this study, in order to find robust SSR markers associated with TGW trait and mine elite accessions in rice, we investigated the TGW trait across six environments using a natural population consisted of 462 accessions, and then performed association mapping using both SSR and SNP markers. Using the six datasets from the six environments and their best linear unbiased estimator, we identified eight TGW associated SSR markers, with three environmentally stable and one newly found, on five chromosomes. The associated markers have genetic effect from 3.44% to 20.84%, and two of them carry stable elite allele with positive effect across different environments. Candidate interval association mapping using re-sequencing derived SNP/InDel markers further confirms the TGW-SSR association, and also suggests that 3 TGW-SSR associations were high confident in intervals of size from 176 to 603 kb. These results not only shed more lights on the genetics of TGW trait, but also suggest that the multi-allelic SSR markers should be used as an alternative power tool in gene or QTL mapping.

A high-throughput <i>S-RN</i>ase genotyping method for apple

Knowledge of the genotypes for the self-incompatibility locus (S-locus) in apple varieties and in genotypes being used as parents is critical for breeding and commercial production. We present a high-throughput set of molecular markers for the identification of 13 common S-RNase alleles (S1, S2, S3, S5, S7, S8, S9, S10, S20, S23, S24, S25 and S28). This set is composed of seven allele-specific quantitative PCR-based High-Resolution Melting assays and four multi-allelic SSR markers. Validation of these markers was performed using 86 apple accessions, including cultivars with known S-genotypes and recent commercial varieties arising from the Plant & Food Research (PFR) cultivar breeding programme. We also characterized the S-genotypes of 183 genotypes representing some of the most valuable parents within PFR’s cultivar breeding programme. The results of this work demonstrate the practical usefulness of this marker set to provide accurate cross-compatibility information to optimise choice of pollenisers in commercial apple orchard design, and to identify compatible parents and guide parental selection when executing apple breeding programmes, to optimise fruit crop yield and quality.

Estimation of Molecular Pairwise Relatedness in Autopolyploid Crops.

A suitable pairwise relatedness estimation is key to genetic studies. Several methods are proposed to compute relatedness in autopolyploids based on molecular data. However, unlike diploids, autopolyploids still need further studies considering scenarios with many linked molecular markers with known dosage. In this study, we provide guidelines for plant geneticists and breeders to access trustworthy pairwise relatedness estimates. To this end, we simulated populations considering different ploidy levels, meiotic pairings patterns, number of loci and alleles, and inbreeding levels. Analysis were performed to access the accuracy of distinct methods and to demonstrate the usefulness of molecular marker in practical situations. Overall, our results suggest that at least 100 effective biallelic molecular markers are required to have good pairwise relatedness estimation if methods based on correlation is used. For this number of loci, current methods based on multiallelic markers show lower performance than biallelic ones. To estimate relatedness in cases of inbreeding or close relationships (as parent-offspring, full-sibs, or half-sibs) is more challenging. Methods to estimate pairwise relatedness based on molecular markers, for different ploidy levels or pedigrees were implemented in the AGHmatrix R package.

Comprehensive Identification of Drought Tolerance QTL-Allele and Candidate Gene Systems in Chinese Cultivated Soybean Population.

Drought is one of the most important factors affecting plant growth and productivity. The previous results on drought tolerance (DT) genetic system in soybean indicated a complex of genes not only few ones were involved in the trait. This study is featured with a relatively thorough identification of QTL-allele/candidate-gene system using an efficient restricted two-stage multi-locus multi-allele genome-wide association study, on two comprehensive DT indicators, membership index values of relative plant weight (MPW) and height (MPH), instead of a single biological characteristic, in a large sample (564 accessions) of the Chinese cultivated soybean population (CCSP). Based on 24,694 multi-allele markers, 75 and 64 QTL with 261 and 207 alleles (2–12/locus) were detected for MPW and MPH, explaining 54.7% and 47.1% of phenotypic variance, respectively. The detected QTL-alleles were organized into a QTL-allele matrix for each indicator, indicating DT is a super-trait conferred by two (even more) QTL-allele systems of sub-traits. Each CCSP matrix was separated into landrace (LR) and released cultivar (RC) sub-matrices, which showed significant differentiation in QTL-allele constitutions, with 58 LR alleles excluded and 16 new ones emerged in RC. Using the matrices, optimal crosses with great DT transgressive recombinants were predicted. From the detected QTL, 177 candidate genes were annotated and validated with quantitative Real-time PCR, and grouped into nine categories, with ABA and stress responders as the major parts. The key point of the above results is the establishment of relatively full QTL-allele matrices composed of numerous gene functions jointly conferring DT, therefore, demonstrates the complexity of DT genetic system and potential of CCSP in DT breeding.

Noninvasive prenatal paternity testing by target sequencing microhaps

Microhaplotypes (i.e.,microhaps or MHs) are emerging multi-allelic markers with at least two single nucleotide polymorphisms (SNPs) within ∼ 200 bp that have alleles of the same length and do not generate stutter products. Based on massively parallel sequencing (MPS) technology, microhaps have proven applicability in forensics for different application purposes. Here we evaluate the feasibility of non-invasive prenatal paternity testing (NIPPT) with a panel of polymorphic microhap markers, using cell-free DNA (cfDNA) in the maternal circulation. A custom MPS-based assay targeting 60 microhaps was developed in our previous study. Herein, we applied the developed assay to cfDNA samples in 15 NIPPT cases in the first trimester of pregnancy (6∼13 weeks). The R package relMix was employed for data interpretation, with a regression dropout estimating model. As a result, the targeted sequencing wherein target enrichment is by hybridization capture can be effectively employed for microhap sequencing with cfDNA samples. With the combined use of relMix, the paternity of the biological fathers in 15 cases was correctly determined, with the combined paternity index (CPI) value > 1012. Moreover, the specificity of this approach was validated by the successful paternity exclusion of 3 close relatives (father, full sibling and uncle) of the biological father in one case, and further by the significant separation in CPI distribution between the biological father and 112 unrelated males in each cases. Our results indicate that this MPS-based microhap sequencing strategy could be utilized in NIPPT. This method may contribute to developments in NIPPT and to the resolution of issues related to DNA mixtures of close relatives for specific purposes.

Polymorphism of monogenic scab resistance loci in apple varieties

Background. Monogenic scab resistance is an important trait of apple, useful to plant breeders. DNA markers provide a possibility to differentiate apple cultivars according to individual resistance determinants with high reliability and identify promising genotypes. The present study shows the results of the molecular genetic analysis of apple varieties, targeted at the Rvi2, Rvi4, Rvi6 and Rvi8 monogenic scab resistance loci.Materials and methods. Biological material was represented by apple cultivars of different environmental and geographical origin. Total genomic DNA was extracted from fresh leaves using CTAB methods according to the DArT protocols. The Rvi6 gene was identified with two markers, VfC (STS) and AL07 (SCAR). The presence of the Rvi4 gene was detected with the multiallelic SCAR marker AD13. The Rvi2 and Rvi8 genes were diagnosed with the SCAR marker OPL19.Results and conclusion. The Rvi6 gene was identified in 54.4% of genotypes, of which 91.9% were heterozygous, and 8.1% (cvs. ‘Svezhest’, ‘Freedom’ and ‘GoldRush’) homozygous dominant for this locus. The marker AD13-SCAR was detected in 25.0% of the studied forms (the putative genotype for the resistance gene is Rvi4Rvi4 or Rvi4rvi4). The marker OPL19-SCAR (Rvi2 and Rvi8 genes) was present in 73.5% of the analyzed forms. At least one of the studied molecular markers was present in the genome of 86.8% of genotypes. The appletree cultivars ‘Kandil Orlovsky’, ‘Krasulya’, ‘Sozvezdiye’, ‘Galarina’, ‘Priam’, ‘Redfree’ and ‘Witos’ are characterized by the combination of markers VfC, AL07-SCAR, AD13-SCAR and OPL19-SCAR in one genotype (the putative genotype for the resistance genes is Rvi2(Rvi8)Rvi4Rvi6rvi6). Cvs. ‘Antonovka zimnyaya’, ‘Antonovka krasnaya’, ‘Berkutovskoye’, ‘Geyzer’, ‘Pamyati Nesterova’, ‘Renet Simirenko’, ‘Terentyevka’, ‘Golden Delicious’, and ‘Telemon’ presumably have a homozygous recessive genotype for the studied resistance loci.

First genomic microsatellite markers developed for Platonia insignis (Clusiaceae), a Brazilian fruit tree.

Platonia insignis is a fruit tree native of Brazil with allogamous and asexual reproduction. The production of fruits is mainly obtained by exploitation of natural populations and the impact of genetic structuring on plant production may be evaluated. For this purpose, codominant and multiallelic markers such as microsatellite are the most suitable, but they need to be developed for this species. Thus, the aim of this work was to develop and validate microsatellite markers for P. insignis. We used Roche 454 GS FLX sequencing platform of a single P. insignis genotype and 1702 microsatellite sequences were identified. Based on some pre-requisites, we could develop 50 primer pairs to be tested. Twenty-two primer pairs successfully amplified fragments and they were tested in 31 genotypes of P. insignis that belong to a germplasm bank and were sampled in the northeast of Pará State, Brazil. Thirteen primers were polymorphic and the number of alleles per loci varied from 5 (PI18 and PI27) to 2 (PI08, PI25, PI31, PI33 and PI 37). Expected heterozygosity (HE) varied from 0.74 (PI27) to 0.12 (PI31) and observed heterozygosity (HO) varied from 1.00 (PI25) to 0.00 (PI08, PI31, PI33 and PI37). Principal coordinates could separate the genotypes of P. insignis in clusters and we can conclude that the primers can estimate the genetic diversity of P. insignis populations.

Multiallelic marker system for traceability of Black Slavonian pig meat

Meat from Black Slavonian pig (Crna slavonska, CS), an autochthonous Croatian breed, is used for the production of high-quality products, which makes it an interesting target for meat fraud. The aim of the study was to develop a set of microsatellite markers suitable for precise genetic traceability of the meat originating from this breed. Initially, 23 microsatellite markers were selected and grouped into three multiplex reactions for the genetic characterization of the seven breeds included in the study; subsequently, a set of eight microsatellite markers for traceability of CS pig was created based on the match probability value. The results indicated that when eight highly polymorphic loci were combined, the chance of finding identical genotype in two random individuals was about three in ten million (10−7). This provided the basis for establishing a reliable genetic traceability system for meat originating from CS pigs.

Allele Frequency Difference AFD⁻An Intuitive Alternative to FST for Quantifying Genetic Population Differentiation.

Measuring the magnitude of differentiation between populations based on genetic markers is commonplace in ecology, evolution, and conservation biology. The predominant differentiation metric used for this purpose is FST. Based on a qualitative survey, numerical analyses, simulations, and empirical data, I here argue that FST does not express the relationship to allele frequency differentiation between populations generally considered interpretable and desirable by researchers. In particular, FST (1) has low sensitivity when population differentiation is weak, (2) is contingent on the minor allele frequency across the populations, (3) can be strongly affected by asymmetry in sample sizes, and (4) can differ greatly among the available estimators. Together, these features can complicate pattern recognition and interpretation in population genetic and genomic analysis, as illustrated by empirical examples, and overall compromise the comparability of population differentiation among markers and study systems. I argue that a simple differentiation metric displaying intuitive properties, the absolute allele frequency difference AFD, provides a valuable alternative to FST. I provide a general definition of AFD applicable to both bi- and multi-allelic markers and conclude by making recommendations on the sample sizes needed to achieve robust differentiation estimates using AFD.

Development of a Molecular Marker Linked to the A4 Locus and the Structure of HD Genes in Pleurotus eryngii

Allelic differences in A and B mating-type loci are a prerequisite for the progression of mating in the genus Pleurotus eryngii; thus, the crossing is hampered by this biological barrier in inbreeding. Molecular markers linked to mating types of P. eryngii KNR2312 were investigated with randomly amplified polymorphic DNA to enhance crossing efficiency. An A4-linked sequence was identified and used to find the adjacent genomic region with the entire motif of the A locus from a contig sequenced by PacBio. The sequence-characterized amplified region marker 7-2299 distinguished A4 mating-type monokaryons from KNR2312 and other strains. A BLAST search of flanked sequences revealed that the A4 locus had a general feature consisting of the putative HD1 and HD2 genes. Both putative HD transcription factors contain a homeodomain sequence and a nuclear localization sequence; however, valid dimerization motifs were found only in the HD1 protein. The ACAAT motif, which was reported to have relevance to sex determination, was found in the intergenic region. The SCAR marker could be applicable in the classification of mating types in the P. eryngii breeding program, and the A4 locus could be the basis for a multi-allele detection marker.

Genetic variation in Hydrangea macrophylla (Thunb.) Ser. in Russia based on simple sequence repeat markers

Genetic diversity and genetic relationships among 39 accessions of Hydrangea macrophylla (Thunb.) Ser. were analyzed using 38 previously developed simple sequence repeat markers (SSRs). A total of 38 polymorphic primers representing 166 bands with an average of 4.53 polymorphic bands per primer were selected. The number of alleles detected per locus ranged from two to eight with a total of 163 alleles amplified. The size of the amplified fragments ranged from 70 to180 base pairs. The effective multiallelic markers with high level of heterozygosity (more than 0.7) and effective number of alleles (more than 3.5) were identified. In this study nine SSR markers showed clear polymorphisms. The dendrogram grouped all hybrids in three major clusters, and two of these clusters included only mophead cultivars. The lacecap cultivars clustered more closely to each other. The results of this research could be used in breeding programs of H. macrophylla.

Forensic applicability of multi-allelic InDels with mononucleotide homopolymer structures.

Insertion/deletion polymorphisms (InDels), which possess the characteristics of low mutation rates and a short amplicon size, have been regarded as promising markers for forensic DNA analysis. InDels can be classified as bi-allelic or multi-allelic, depending on the number of alleles. Many studies have explored the use of bi-allelic InDels in forensic applications, such as individual identification and ancestry inference. However, multi-allelic InDels have received relatively little attention. In this study, InDels with 2-6 alleles and a minor allele frequency ≥0.01, in Chinese Southern Han (CHS), were retrieved from the 1000 Genomes Project Phase III. Based on the structural analysis of all retrieved InDels, 17 multi-allelic markers with mononucleotide homopolymer structures were selected and combined in one multiplex PCR reaction system. Sensitivity, species specificity and applicability in forensic case work of the multiplex were analyzed. A total of 218 unrelated individuals from a Chinese Han population were genotyped. The combined discriminatory power (CDP), the combined match probability (CMP) and the cumulative probability of exclusion (CPE) were 0.9999999999609, 3.91E-13 and 0.9956, respectively. The results demonstrated that this InDel multiplex panel was highly informative in the investigated population and most of the 26 populations of the 1000 Genomes Project. The data also suggested that multi-allelic InDel markers with monomeric base pair expansions are useful for forensic applications.

SNP-haplotypes: An accurate approach for parentage and relatedness inference in gilthead sea bream (Sparus aurata)

Pedigree information among individuals has become a key factor in the correct management and conservation of wild populations, as well as captive stocks. Despite the growing interest in the identification and application of single nucleotide polymorphism (SNP) markers, to date, microsatellite loci continues to be considered as the genetic marker par excellence to establish the degree of relationship among individuals. In fact, although high-density SNP panels are a highly accurate tool for inferring kinship relationships, at small-scale, with only a reduced number of SNPs involved, it is difficult to preserve that accuracy due to the bi-allelic nature of this genetic marker.The present study has evaluated the accuracy of SNP-haplotypes (genotypic combination of single SNPs located in the same gene) as parentage and relatedness tool in gilthead sea bream (Sparus aurata). Initially, by direct sequencing of 11 genes in a set of 30 unrelated individuals with heterogeneous origin, a total of 398 putative SNPs were identified and, by means of a filtering procedure to remove false positive and SNPs in a very low frequency, 164 SNPs were selected for the final panel. Using the iPLEX Gold MassARRAY technology, a subset of 58 SNPs located in 7 genes were genotyped in 424 individuals organized into two broodstocks (54 breeders and 370 offspring with pedigree previously inferred by microsatellite loci). From the obtained genotype data, a SNP-haplotype reconstruction was carried out for each gene. According to this approach, 58 biallelic single SNPs were turned into 7 multi-allelic markers (1 gene = 1 marker) whose allele (haplotype) number ranged from 3 to 41. This SNP-haplotypes resolved parentage assignment with an accuracy higher than 99%, resulting in a 10.5% and 3.5% more accuracy than the set of 58 SNPs and 9 microsatellite loci, respectively. Likewise, under a scenario in which ancestral information was not available, SNP-haplotypes showed an accuracy similar than microsatellite loci for discriminating unrelated individuals. Using this approach, a proportion close to 94% of unrelated individuals correctly classified for the coefficient of relationship equal to zero (theoretically expected relatedness value between unrelated individuals) was achieved. The 6% of individuals, misclassified as unrelated, were largely half-sibs since the full-sibs did not exceed 0.03%. In conclusion, we report herein that SNP-haplotypes approach represents a highly efficient alternative to microsatellite loci to infer parentage and assess relatedness.

S-genotype characterisation of 10 Kernel-apricots native to China

ABSTRACTThe reproductive mechanism of Kernel-apricot involves Gametophytic self-incompatibility (GSI) which is under S-allele control. It encodes a polymorphic pistil ribonuclease (S-RNase), which is multiallelic and ideal markers for S-genotypes characterisation. In this study, six S-RNase primers were used to identify theS-genotypes of 10 Kernel-apricot, including three self-design primers and three universal primers. Ten S-alleles were identified in 10 Kernel-apricot through sequencing and comparing in NCBI. Moreover, some Kernel-apricot S-genotypes were confirmed by experiment of fruit-setting ratio and pollen tube growth. In conclusion, S-genotypes information of Kernel-apricot will be helpful for breeders and growers to plan compatible hybridised combination for ensuring effective pollination and high fruit-setting ratio.

Morphological and Molecular Data Reveal Three Distinct Populations of Indian Wild Rice Oryza rufipogon Griff. Species Complex.

Wild relatives of crops possess adaptive mutations for agronomically important traits, which could play significant role in crop improvement for sustainable agriculture. However, global climate change and human activities pose serious threats to the natural habitats leading to erosion of genetic diversity of wild rice populations. The purpose of this study was to explore and characterize India’s huge untapped wild rice diversity in Oryza rufipogon Griff. species complex from a wide range of ecological niches. We made strategic expeditions around diversity hot spots in 64 districts of nine different agro-climatic zones of the country and collected 418 wild rice accessions. Significant variation was observed among the accessions for 46 morphological descriptors, allowing classification into O. nivara, O. rufipogon, and O. sativa f. spontanea morpho-taxonomic groups. Genome-specific pSINE1 markers confirmed all the accessions having AA genome, which were further classified using ecotype-specific pSINE1 markers into annual, perennial, intermediate, and an unknown type. Principal component analysis revealed continuous variation for the morphological traits in each ecotype group. Genetic diversity analysis based on multi-allelic SSR markers clustered these accessions into three major groups and analysis of molecular variance for nine agro-climatic zones showed that 68% of the genetic variation was inherent amongst individuals while only 11% of the variation separated the zones, though there was significant correlation between genetic and spatial distances of the accessions. Model based population structure analysis using genome wide bi-allelic SNP markers revealed three sub-populations designated ‘Pro-Indica,’ ‘Pro-Aus,’ and ‘Mid-Gangetic,’ which showed poor correspondence with the morpho-taxonomic classification or pSINE1 ecotypes. There was Pan-India distribution of the ‘Pro-Indica’ and ‘Pro-Aus’ sub-populations across agro-climatic zones, indicating a more fundamental grouping based on the ancestry closely related to ‘Indica’ and ‘Aus’ groups of rice cultivars. The Pro-Indica population has substantial presence in the Eastern Himalayan Region and Lower Gangetic Plains, whereas ‘Pro-Aus’ sub-population was predominant in the Upper Gangetic Plains, Western Himalayan Region, Gujarat Plains and Hills, and Western Coastal Plains. In contrast ‘Mid-Gangetic’ population was largely concentrated in the Mid Gangetic Plains. The information presented here will be useful in the utilization of wild rice resources for varietal improvement.

Construction and forensic genetic characterization of 11 autosomal haplotypes consisting of 22 tri-allelic indels

Insertion/deletion polymorphisms (indels), which combine the advantages of both short tandem repeats and single-nucleotide polymorphisms, are suitable for parentage testing. To overcome the limitations of the low polymorphism of di-allelic indels, we constructed a set of haplotypes with physically linked, multi-allelic indels. Candidate haplotypes were selected from the 1000 Genomes Project database, and were subject to the following criteria for inclusion: (i) each marker must have a minimum allele frequency (MAF) of ≥0.1 in the Han population of China; (ii) markers must exist in a non-coding region; (iii) the physical distance between a pair of candidate indels must be <500 bp; (iv) the allele length variation of each indel from 1 to 20 bp; (v) different haplotypes must be located on different chromosomes or chromosomal arms, or be more than 10 Mb apart if on the same chromosomal arm; and (vi) they must not be located across a recombination hotspot. A multiplex system with 11 haplotype markers, comprising 22 tri-allelic indel loci distributed over 10 chromosomes was developed. To validate the multiplex panel, we investigated the haplotype distribution in sets of two and three-generation pedigrees. The results demonstrated that the haplotypes consisting of multi-allelic indel markers exhibited higher polymorphism than a single indel locus, and thus provide Supplementary information for forensic kinship identification.

Microhaplotypes provide increased power from short‐read DNA sequences for relationship inference

The accelerating rate at which DNA sequence data are now generated by high-throughput sequencing instruments provides both opportunities and challenges for population genetic and ecological investigations of animals and plants. We show here how the common practice of calling genotypes from a single SNP per sequenced region ignores substantial additional information in the phased short-read sequences that are provided by these sequencing instruments. We target sequenced regions with multiple SNPs in kelp rockfish (Sebastes atrovirens) to determine "microhaplotypes" and then call these microhaplotypes as alleles at each locus. We then demonstrate how these multi-allelic marker data from such loci dramatically increase power for relationship inference. The microhaplotype approach decreases false-positive rates by several orders of magnitude, relative to calling bi-allelic SNPs, for two challenging analytical procedures, full-sibling and single parent-offspring pair identification. We also show how the identification of half-sibling pairs requires so much data that physical linkage becomes a consideration, and that most published studies that attempt to do so are dramatically underpowered. The advent of phased short-read DNA sequence data, in conjunction with emerging analytical tools for their analysis, promises to improve efficiency by reducing the number of loci necessary for a particular level of statistical confidence, thereby lowering the cost of data collection and reducing the degree of physical linkage amongst markers used for relationship estimation. Such advances will facilitate collaborative research and management for migratory and other widespread species.

Genomic Prediction of Autogamous and Allogamous Plants by SNPs and Haplotypes

The implementation of single‐nucleotide polymorphism (SNP)‐based genomic selection has demonstrated great predictive potential in plants. However, its application is sometimes limited to the biallelism of the marker. In this context, the use of haplotype blocks as multiallelic markers might improve genomic prediction. This study was performed to compare the predictive ability of Bayesian genomic prediction models using haplotypes (confidence interval and four‐gamete), individual SNPs, and sets of SNPs selected according to haplotype construction. The use of haplotype matrices increased the predictive ability and selection coincidence with the phenotypic selection for the maize (Zea mays L.) breeding population. However, this was not observed for the rice (Oryza sativa L.) population, in which the use of the nonreduced SNP matrix was more efficient. Overall, the use of reduced SNP matrices did not lead to better predictive abilities. No difference was observed between the genomic prediction methods used. We found that the use of haplotypes has potential to increase predictive ability of genomic prediction in breeding populations of allogamous plants or plants with high multiallelism.

Exploring and Harnessing Haplotype Diversity to Improve Yield Stability in Crops.

In order to meet future food, feed, fiber, and bioenergy demands, global yields of all major crops need to be increased significantly. At the same time, the increasing frequency of extreme weather events such as heat and drought necessitates improvements in the environmental resilience of modern crop cultivars. Achieving sustainably increase yields implies rapid improvement of quantitative traits with a very complex genetic architecture and strong environmental interaction. Latest advances in genome analysis technologies today provide molecular information at an ultrahigh resolution, revolutionizing crop genomic research, and paving the way for advanced quantitative genetic approaches. These include highly detailed assessment of population structure and genotypic diversity, facilitating the identification of selective sweeps and signatures of directional selection, dissection of genetic variants that underlie important agronomic traits, and genomic selection (GS) strategies that not only consider major-effect genes. Single-nucleotide polymorphism (SNP) markers today represent the genotyping system of choice for crop genetic studies because they occur abundantly in plant genomes and are easy to detect. SNPs are typically biallelic, however, hence their information content compared to multiallelic markers is low, limiting the resolution at which SNP–trait relationships can be delineated. An efficient way to overcome this limitation is to construct haplotypes based on linkage disequilibrium, one of the most important features influencing genetic analyses of crop genomes. Here, we give an overview of the latest advances in genomics-based haplotype analyses in crops, highlighting their importance in the context of polyploidy and genome evolution, linkage drag, and co-selection. We provide examples of how haplotype analyses can complement well-established quantitative genetics frameworks, such as quantitative trait analysis and GS, ultimately providing an effective tool to equip modern crops with environment-tailored characteristics.

Comparative assessment of SSR and SNP markers for inferring the population genetic structure of the common fungus Armillaria cepistipes

During the last years, simple sequence repeats (SSRs, also known as microsatellites) and single-nucleotide polymorphisms (SNPs) have become the most popular molecular markers for describing neutral genetic variation in populations of a wide range of organisms. However, only a limited number of studies has focused on comparing the performance of these two types of markers for describing the underlying genetic structure of wild populations. Moreover, none of these studies targeted fungi, the group of organisms with one of the most complex reproductive strategies. We evaluated the utility of SSRs and SNPs for inferring the neutral genetic structure of Armillaria cepistipes (basidiomycetes) at different spatial scales. For that, 407 samples were collected across a small (150 km2) area in the Ukrainian Carpathians and a large (41 000 km2) area in the Swiss Alps. All isolates were analyzed at 17 SSR loci distributed throughout the whole genome and at 24 SNP loci located in different single-copy conserved genes. The two markers showed different patterns of structure within the two spatial scales studied. The multi-allelic SSR markers seemed to be best suited for detecting genetic structure in indigenous fungal populations at a rather small spatial scale (radius of ~50-100 km). The pattern observed at SNP markers rather reflected ancient divergence of distant (~1000 km) populations that in addition are separated by mountain ranges. Despite these differences, both marker types were suitable for detecting the weak genetic structure of the two A. cepistipes populations investigated.