DNA Marker Data Research Articles

Comparison of DNA marker and pedigree-based methods of genetic analysis in plantain and banana (Musa spp.) clones. II. Predicting hybrid performance

Pedigree and DNA marker-based methods were used to predict the performance of triploid progeny from tetraploid-diploid crosses, based on parental heterozygosity, genetic relatedness, and expected contribution to their progeny. There was no significant correlation between parental and progeny performance. Prediction of progeny bunch weight was best when based on genealogical distance and equal parental contribution. Predicted fruit size was most accurate when DNA marker data were used and the assumption of an unequal parental contribution was made. Consideration of parental heterozygosity produced larger residuals for all traits. No statistically significant differences were found between the mean residuals obtained under the assumption of an equal vs an unequal contribution of the 4x and 2x genotypes to their 3x progeny, regardless of the method used to estimate genetic relationships.

Proportion of genes survived in offspring conditional on inheritance of flanking markers.

In mammalian genetics and perhaps in human genetics as well, it is an interesting question as to how many offspring are needed in order to have a desired chance of preserving part of the entire genome of an individual. A more practical and perhaps more important question is: given k children and DNA marker data on a particular region of interest, what proportion of one's genes has been actually passed on to his children? To answer this question, I define the concept of identity by descent proportion, or IBDP for short. The IBDP is defined to be the proportion of genetic material shared identical by descent by a group of relatives in a specified chromosomal region. I provide a novel approach to computing the mean and variance of IBDP for k (> or = 2) half-sibs based on marker data, thus providing a means to compute the mean and variance of proportion of genes survived. I first show that each chromosome in an offspring can be represented by a two-state Markov chain, with the time parameter being the map distance along the chromosome. On this basis, I will show that IBDP can be written as a stochastic integral and that the computation of the EIBDP can be reduced to evaluating an integral of some elementary functions. Numerical examples are provided to illustrate the calculation.

An assessment of the use of flanking DNA markers for fra(X) syndrome carrier detection and prenatal diagnosis.

One hundred and three individuals in 11 unrelated families with the fragile-X [fra(X)] syndrome were tested for polymorphisms identified by probes flanking the fra(X) site at Xq27.3. Two probes distal and 2 proximal to the fra(X) site were used. Thirteen known female carriers were analyzed retrospectively. DNA markers gave probabilities of carrying the mutation of 99% in 1 female, 89% in 8 females, and 10-55% in the other 4 females. We also estimated the probability of having inherited the mutation for 16 individuals of unknown fra(X) status using DNA markers and corrections for incomplete penetrance. The DNA marker test gave risks for females of 1-6% (7 females), 15% (1 female), and 97% (1 female). In males the risks were 1-3% (6 males) and 91% (1 male). In 3 families, DNA marker data were used to calculate probabilities of greater than or equal to 98.5% that transmission of the fra(X) mutation had occurred through normal males. In the retrospective studies, only 1 of 7 retarded males could have been diagnosed prenatally as having the fra(X) mutation with a probability of 99%. DNA marker analysis was uninformative in 5 of these males. When fra(X) carrier status cannot be established by chromosome analysis, DNA marker studies provide an alternative test that can be used to calculate individual risks more precisely. However, linkage analysis of the probe loci in these 11 families suggests that the recombination frequency between the fra(X) locus and the factor IX gene (F9) and DXS52 may be greater than previously suggested. Until the true recombination frequencies are established and the question of heterogeneity among families is fully analyzed, caution in using DNA markers as a predictive test is advised.