Soybean pedigree analysis using map-based molecular markers: recombination during cultivar development

An analysis of the genome structure of soybean cultivars was conducted to determine if cultivars are composed of large regions of chromosomes inherited intact from one parent (indicative of minimal recombination) or if the chromosomes are a mixture of one parent's DNA interspersed with the DNA from the other parent (indicative of maximal recombination). Twenty-one single-cross-derived and 5 single-backcross-derived soybean cultivars and their immediate parents (47 genotypes) were analyzed at 89 RFLP loci to determine the minimal number and distribution of recombination events detected. Cultivars derived from single-cross and single-backcross breeding programs showed an average of 5.2 and 8.0 recombination events per cultivar, respectively. A homogeneity Chi-square test based upon a Poisson distribution of recombination events across 13 linkage groups indicated that the number of recombinations observed among linkage groups was random for the single-cross cultivars, but not for the single-backcross-derived cultivars. A twotailed t-test demonstrated that for some linkage groups, the number of recombinations per map unit exceeded the confidence interval developed from a t-distribution of recombinations standardized for map unit distance. Paired t-tests of the number of recombinations observed between linkage-group ends and the mid-portion of the linkage groups indicated that during the development of the cultivars analyzed in this study more recombinations were associated with the ends of linkage groups than with the middle region. Detailed analysis of each linkage group revealed that large portions of linkage groups D, F, and G were inherited intact from one parent in several cultivars. A portion of linkage group G, in contrast, showed more recombination events than expected, based on genetic distance. These analyses suggest that breeders may have selected against recombination events where agronomically favorable combinations of alleles are present in one parent, and for recombination in areas where agronomically favorable combinations of alleles are not present in either parent.Names are necessary to report factually on the available data; however, the USDA neither guarantees nor warrants the standard of the product, and the use of the name by the USDA implies no approval of the product to the exclusion of others that may also be available. Contribution of the Midwest Area, USDA-ARS, Project No. 3236 of the Iowa Agriculture and Home Economics Experiment Station, Ames, IA 50011. Journal Paper No. J-16533     

Mapping quantitative trait loci with dominant markers in four-way crosses

 A common problem in mapping quantitative trait loci (QTLs) is that marker data are often incomplete. This includes missing data, dominant markers, and partially informative markers, arising in outbred populations. Here we briefly present an iteratively re-weighted least square method (IRWLS) to incorporate dominant and missing markers for mapping QTLs in four-way crosses under a heterogeneous variance model. The algorithm uses information from all markers in a linkage group to infer the QTL genotype. Monte Carlo simulations indicate that with half dominant markers, QTL detection is almost as efficient as with all co-dominant markers. However, the precision of the estimated QTL parameters generally decreases as more markers become missing or dominant. Notable differences are observed on the standard deviation of the estimated QTL position for varying levels of marker information content. The method is relatively simple so that more complex models including multiple QTLs or fixed effects can be fitted. Finally, the method can be readily extended to QTL mapping in full-sib families. Received: 16 June 1998 / Accepted: 29 September 1998     

Maximum-likelihood models for mapping genetic markers showing segregation distortion. 2. F2 populations

In F₂ populations, gametic and zygotic selection may affect the analysis of linkage in different ways. Therefore, specific likelihood equations have to be developed for each case, including dominant and codominant markers. The asymptotic bias of the classical estimates are derived for each case, in order to compare them with the standard errors of the suggested estimates. We discuss the utility and the efficiency of a previous model developed for dominant markers. We show that dominant markers provide very poor information in the case of segregation distortion and, therefore, should be used with circumspection. On the other hand, the estimation of recombination fractions between codominant markers is less affected by selection than is that for dominant markers. We also discuss the analysis of linkage between dominant and codominant markers.     

The effects of selective genotyping on estimates of proportion of recombination between linked quantitative trait loci

Selective genotyping is the marker assay of only the more extreme phenotypes for a quantitative trait and is intended to increase the efficiency of quantitative trait loci (QTL) mapping. We show that selective genotyping can bias estimates of the recombination frequency between linked QTLs — upwardly when QTLs are in repulsion phase, and downwardly when QTLs are in coupling phase. We examined these biases under simple models involving two QTLs segregating in a backcross or F₂ population, using both analytical models and computer simulations. We found that bias is a function of the proportion selected, the magnitude of QTL effects, distance between QTLs and the dominance of QTLs. Selective genotyping thus may decrease the power of mapping multiple linked QTLs and bias the construction of a marker map. We suggest a large proportion than previously suggested (50%) or the entire population be genotyped if linked QTLs of large effects (explain > 10% phenotypic variance) are evident. New models need to be developed to explicitly incorporate selection into QTL map construction.     

Analysis of genetic recombination in maize populations using molecular markers

Summary Variation in recombination rate is important to plant breeders since a major objective is to obtain favorable recombinants of linked genes. The ability to increase recombination (R) in circumstances in which favorable and unvavorable genes are linked (Corn Belt x exotic populations) and to decrease recombination when many favorable genes are linked (narrow-based, elite populations) would be of immense value. However, the concept of variation in recombination frequencies between linked genes has received limited attention despite its implications in breeding and genetic linkage studies. Molecular techniques have allowed better estimations of this variation. In this study, attempts were made to characterize: (1) the R values in the Pgm1-Adh1 and Adh1-Phi1 adjacent regions of chromosome 1 and the Idh2-Mdh2 region of chromosome 6 in F₂ families of three maize (Zea mays L.) populations; (2) the environmental effect on R values of F₂s from two populations. One population, NSO, was a Corn Belt synthetic, and the other two populations, CBMEX3 and CBCAR5, were composites from crosses between Corn Belt and exotic germ-plams.Wide ranges of estimated recombination ( ) values were observed among families in each population for all three chromsomal regions. The distribution of values for the Pgm1-Adh1 region showed that the F₂ families of each population fell into two broad categories: 0.30–0.50 and 0.02–0.20. No intermediates (0.21–0.29) were found. The distributions were almost normal for the Adh1-Phi1 and the Idh2-Mdh2 regions. It would appear that the major dispersion in the Pgm1-Adh1 region was controlled by the effects of a single gene, while the Adh1-Phi1 and Idh2-Mdh2 regions were only affected by polygenes. No correlation was found between recombination values of the two adjacent regions, indicating that the genes affecting recombination for the Pgm1-Adh1 region may be specific for that region.For the Pgm1-Adh1 region, no differences in values were found among the three populations. For the Adh1-Phi1 region, frequencies of CBMEX3 and NSO were not significantly different, but both had significantly greater values than CBCAR5. For the Idh2-Mdh2 region, CBMEX3 was significantly different from NSO. There were significant differences between some paired F₂ families within each population for each chromosome region.No significant differences in response to the two environments were detected in CBMEX3 and NSO for either region in chromosome 1.Published as Journal Paper No. 9498 of the Nebraska Agric Res Div, University of Nebraska, Lincoln, Neb. Research supported in part by USDA Competitive Grant 87-CRCR-2359     

Segregation of random amplified DNA markers in F1 progeny of conifers

Summary The recently developed approach to deriving genetic markers via amplification of random DNA segments with single primers of arbitrary nucleotide sequence was tested for its utility in genetic linkage mapping studies with conifers. Reaction conditions were optimized to reproducibly yield clean and specific amplification products. Template DNA from several genotypes of Douglas-fir (Pseudotsuga menziesii) and white spruce (Picea glauca) were tested against eight ten-base oligonucleotide primers. Most of the tested primer/parent tree combinations yielded polymorphic PCR products (RAPD markers). Selected primers were then used in PCR reactions with template DNA isolated from offspring in Douglas-fir and black spruce diallel crosses among the same parental lines. The diallel study confirmed the appropriate inheritance of RAPD markers in the F₁ generation. The value of these dominant RAPD markers for genetic linkage mapping in trees was established from both theoretical and applied perspectives.     

Comparison of RAPD and RFLP markers for mapping F2 generations in maize (Zea mays L.)

The F₂ generations from two maize crosses were used to compare the ability of RAPD and RFLP marker systems to create a genetic linkage map. Both RFLPs and RAPDs were shown to provide Mendelian-type markers. Most of the RFLPs (80%) could be placed with a good level of certainty (LOD>4) on the genetic linkage map. However, because of their dominant nature, only between 37% and 59% of the RAPDs could be placed with such a LOD score. The use of combined data from RFLPs and RAPDs increases the level of information provided by RAPDs and allows the creation of a combined RFLP/RAPD genetic linkage map. Thus, the RAPD technique was found to be a powerful method to provide improved probes coverage on a previously created RFLP map and to locate markers linked to chromosomal regions of interest.     

Genetic diversity in Vicia amoena (Fabaceae) germplasm resource in China using SRAP and ISSR markers

The genetic diversity in 17 germplasms of Vicia amoena L. from north China was analyzed using SRAP and ISSR markers. Three hundred and sixty-eight (94.11%) polymorphic bands (211 and 157 obtained from 20 pairs of SRAP and ISSR primers, respectively) were scored. Although SRAP was more effective than ISSR markers with higher PIC, RP and larger variation range of genetic distance, both the markers were useful for assessing V. amoena genetic diversity. Cluster analysis showed that the 17 germplasms were clustered into 5 groups. The results of principal coordinate analysis supported UPGMA clustering. The germplasms from source areas where the annual average temperature ranged from −1.0 to 5 °C exhibited the highest level of genetic diversity with the highest PPI, I and H. These results have important implications in genome mapping, breeding purposes, and germplasm conservation.     

水稻DH群体的分子连锁图谱及基因组分析

利用扩大的籼粳杂交来源（窄叶青８号×京系１７）的水稻（ＯｒｙｚａｓａｔｉｖａＬ．）加倍单倍体（ＤＨ）群体,构建了包含４４４个位点的分子连锁图谱,覆盖水稻基因组１９６２ｃＭ（ｃｅｎｔｉＭｏｒｇｏｎ）,标记间的平均图距小于５ｃＭ。此图谱包括２７６个ＲＦＬＰ标记、３４个ＲＡＰＤ标记、８９个微卫星标记、１０个ＡＦＬＰ标记、２６个端粒重复相关序列（ＴＡＳ）标记以及９个同工酶标记。该遗传图谱与其它的水稻高密度遗传图谱具有较高的可比性,并有自己的特点,适于进行各种持续性的遗传学研究     

Genetic relationship of Porteresia coarctata Tateoka using molecular markers

ABSTRACT

Twenty-one species belonging to Oryza, including wild rices, were compared with a tetraploid (2n=48) halophytic wild rice relative, Porteresia coarctata Tateoka (=Oryza coarctata) for the genetic relatedness using AFLP and RAPD markers. Diploid and tetraploid groups were clearly separated except in the case of a few species where the clustering was unique and different. The molecular analysis has helped in positioning Porteresia in the vicinity of other wild rice species, and to better understand the pattern of species differentiation in Oryza. From our study, O. australiensis seems to be related to P. coarctata; thus, O. australiensis may be an effective “bridge” species in transferring genetic traits from P. coarctata to O. sativa. The usefulness of molecular marker systems for studying polymorphism and classification, and in clarifying genetic relationships between wild species has been confirmed.     

Genetic Molecular Linkage Map Construction and Genome Analysis of Rice Doubled Haploid Population

A high density genetic linkage map comprised of aA. 4 loci was constructed from a doubled haploid population derived from a inter-subspecific cross between an Oryza satire L. ssp. Indica vari.t.v ("Zhaiyeqing 8") and a japonica variety ("Jingxi 17"). The genetic map consisted of 276 RFLP markers, 34 RAPD markers, 89 microsatellite markers, 10 AFLP markers, 26 markers based on telomeric repetitive associated sequence (TAS) and 9 isozyme markers. This genetic map was highly comparable with other high density rice genetic maps and had its unique feature which meritted it suitable for sustained genetic analysis.     

Mapping quantitative trait loci with dominant and missing markers in various crosses from two inbred lines

Dominant phenotype of a genetic marker provides incomplete information about the marker genotype of an individual. A consequence of using this incomplete information for mapping quantitative trait loci (QTL) is that the inference of the genotype of a putative QTL flanked by a marker with dominant phenotype will depend on the genotype or phenotype of the next marker. This dependence can be extended further until a marker genotype is fully observed. A general algorithm is derived to calculate the probability distribution of the genotype of a putative QTL at a given genomic position, conditional on all observed marker phenotypes in the region with dominant and missing marker information for an individual. The algorithm is implemented for various populations stemming from two inbred lines in the context of mapping QTL. Simulation results show that if only a proportion of markers contain missing or dominant phenotypes, QTL mapping can be almost as efficient as if there were no missing information in the data. The efficiency of the analysis, however, may decrease substantially when a very large proportion of markers contain missing or dominant phenotypes and a genetic map has to be reconstructed first on the same data as well. So it is important to combine dominant markers with codominant markers in a QTL mapping study. This revised version was published online in July 2006 with corrections to the Cover Date.     

Molecular characterization of olive (Olea europaea L.) Sicilian cultivars using SSR markers

Olive (Olea europaea L.) is one of the economically most important fruit crops for the Mediterranean area, with production being mainly destined to oil extraction. In Sicily, olive has been cultivated since ancient times and its germplasm is characterized by a wide genetic diversity that could be related to its domestication and spread in ancient times, and to some reproductive biological peculiarities as self-incompatibility. This analysis was conducted on 65 genotypes with the purpose of characterizing a large collection of Sicilian accessions (47 genotypes) and to compare them with varieties coming from Southern Italy and from the most important countries of the Mediterranean basin. With this aim we used 8 simple sequence repeat (SSR) markers, which detected a total of 74 alleles and identified an average of 19.5 genotypes in the population investigated. A larger variability than expected was found in the analyzed genotypes, some synonymies already reported in literature were confirmed, but also some cultivars considered as identical were discriminated such as in the case of Castriciana, Ogliarola messinese and Passalunara. The whole study revealed a wide intraspecific variability within the gene pool examined, independently from the geographical origin.     

Analysis of arthropod bloodmeals using molecular genetic markers

Little is known about the transmission dynamics of human malaria and other vector-borne diseases, partly because of the limited availability and distribution of appropriate tools for quantifying human-mosquito contact rates. Recent developments in molecular biology have allowed a significant increase in the efficacy and reliability of bloodmeal identification, and DNA-based molecular markers are now being harnessed for typing arthropod bloodmeals. The extent to which these markers have been used for analysis of mosquito bloodmeals and the potential they might have for the future is discussed, and the contributions that the advent of PCR has made are examined here.     

A Bayesian approach to inferring population structure from dominant markers

Molecular markers derived from polymerase chain reaction (PCR) amplification of genomic DNA are an important part of the toolkit of evolutionary geneticists. Random amplified polymorphic DNA markers (RAPDs), amplified fragment length polymorphisms (AFLPs) and intersimple sequence repeat (ISSR) polymorphisms allow analysis of species for which previous DNA sequence information is lacking, but dominance makes it impossible to apply standard techniques to calculate F-statistics. We describe a Bayesian method that allows direct estimates of FST from dominant markers. In contrast to existing alternatives, we do not assume previous knowledge of the degree of within-population inbreeding. In particular, we do not assume that genotypes within populations are in Hardy-Weinberg proportions. Our estimate of FST incorporates uncertainty about the magnitude of within-population inbreeding. Simulations show that samples from even a relatively small number of loci and populations produce reliable estimates of FST. Moreover, some information about the degree of within-population inbreeding (FIS) is available from data sets with a large number of loci and populations. We illustrate the method with a reanalysis of RAPD data from 14 populations of a North American orchid, Platanthera leucophaea.     

Genetic fingerprinting of pigeonpea [Cajanus cajan (L.) Millsp.] and its wild relatives using RAPD markers

Randomly amplified polymorphic DNA (RAPD) markers were used for the identification of pigeonpea [Cajanus cajan (L.) Millsp.] cultivars and their related wild species. The use of single primers of arbitrary nucleotide sequence resulted in the selective amplification of DNA fragments that were unique to individual accessions. The level of polymorphism among the wild species was extremely high, while little polymorphism was detected within Cajanus cajan accessions. All of the cultivars and wild species under study could be easily distinguished with the help of different primers, thereby indicating the immense potential of RAPD in the genetic fingerprinting of pigeonpea. On the basis of our data the genetic relationship between pigeonpea cultivars and its wild species could be established.NCL Communication No. 6062     

Genetic characterization of Latin-American Creole cattle using microsatellite markers

Genetic diversity in and relationships among 26 Creole cattle breeds from 10 American countries were assessed using 19 microsatellites. Heterozygosities, F-statistics estimates, genetic distances, multivariate analyses and assignment tests were performed. The levels of within-breed diversity detected in Creole cattle were considerable and higher than those previously reported for European breeds, but similar to those found in other Latin American breeds. Differences among breeds accounted for 8.4% of the total genetic variability. Most breeds clustered separately when the number of pre-defined populations was 21 (the most probable K value), with the exception of some closely related breeds that shared the same cluster and others that were admixed. Despite the high genetic diversity detected, significant inbreeding was also observed within some breeds, and heterozygote excess was detected in others. These results indicate that Creoles represent important reservoirs of cattle genetic diversity and that appropriate conservation measures should be implemented for these native breeds in order to minimize inbreeding and uncontrolled crossbreeding.     

Estimating pairwise relatedness from dominant genetic markers

Knowledge of the genetic relatedness between a pair of individuals is important in many research areas of quantitative genetics, conservation genetics, evolution and ecology. Many estimators have been developed to estimate such pairwise relatedness (r) using codominant markers, such as microsatellites and enzymes. In contrast, only two estimators are proposed to use dominant markers, such as random amplified polymorphic DNAs (RAPDs) and amplified fragment length polymorphisms (AFLPs), in relatedness inference. They are both biased estimators, and their statistical properties and robustness to the sampling errors in allele frequency have not been investigated. In this short paper, I propose two new pairwise relatedness estimators for dominant markers, and compare them in precision, accuracy and robustness to sampling with the two previous estimators using simulations. It was found that the new estimator based on the least squares approach is unbiased when allele frequencies are known or estimated from a sample without correcting for sampling effects. It has, however, a low precision and as a result, an intermediate overall performance among the four estimators in terms of the mean squared deviation (MSD) of estimates from actual values of r. The new estimator based on a similarity index is slightly biased but has generally the lowest MSD among the four estimators compared, regardless of the number of loci, type of actual relationships, allele frequencies known or estimated from samples. Simulations also show that the confidence intervals estimated by bootstrapping are appropriate for different estimators provided that the number of loci used in the estimation is not small.     

Genetic diversity analysis of Pinellia ternata based on SRAP and TRAP markers

An assessment of the genetic diversity and variation of Pinellia ternata collected from 43 populations in China was undertaken using SRAP + TRAP markers. A total of 13 SRAP primers in addition to 3 TRAP primer combinations yielded 292 bands in total of which 286 were polymorphic (98.0%), with an average of 16 for each. The PIC value ranged from 0.88 to 0.95, with a mean polymorphic information content (PIC) of 0.92 over all the primers. A cluster analysis was conducted based on the unweighted pair group method with arithmetic average (UPGMA), and a principle coordinate analysis (PCA) was performed relying on Nei's genetic distance, both of which showed similar outcomes in that the results of clustering did not correlate to the geography locations but showed an association with morphology. An analysis of molecular variance (AMOVA) was performed to detect the source of variation; the results indicated that the main variation existed within populations (67.2%), whereas there was still 32.8% differentiation existing among the populations.     

Multilocus estimation of pairwise relatedness with dominant markers

Estimators for pairwise relatedness designed for dominant markers are derived, based on a genetic model that accounts for the full structure of pairwise relatedness between two individuals at a diploid locus with dominance. They jointly estimate 'relatedness' and 'fraternity', in which case the estimators are inherently multilocus, as at least two loci of differing gene frequency are required. Extensions to cases of zero fraternity and isolation by distance (inbreeding) are also examined. Properties of estimators are examined by simulation and compared to the estimator of Hardy. The most statistical power for pairwise relatedness occurs when roughly half of individuals are the recessive phenotype. Estimation procedures are implemented in the computer program mark.