The detection and estimation of linkage in polyploids using single-dose restriction fragments

Abstract

Restriction fragment length polymorphism (RFLP) linkage maps have been constructed in several major diploid crops. However, construction of RFLP maps directly in polyploids has lagged behind for several reasons: (1) there are a large number of possible genotypes for each DNA probe expected in a segregating population, and these genotypes cannot always be identified readily by their banding phenotypes; and (2) the genome constitutions (allopolyploidy versus autopolyploidy) in many high polyploids are not clearly understood. We present here an analysis of these problems and propose a general method for mapping polyploids based on segregation of single-dose restriction fragments (SDRFS). SDRFs segregate 1:1 (presence: absence) in gametes of heterozygous plants. Hypothetical allopolyploid and autopolyploid species with four ploidy levels of 2n = 4x, 6x, 8x, and 10x, are used to illustrate the procedures for identifying SDRFs, detecting linkages among SDRFs, and distinguishing allopolyploid versus autopolyploids from polyploids of unknown genome constitution. Family size required, probability of linkage, and attributes of different mapping populations are discussed. We estimate that a population size of 75 is required to identify SDRFs with 98% level of confidence for the four ploidy levels. This population size is also adequate for detecting and estimating linkages in the coupling phase for both allopolyploids and autopolyploids, but linkages in the repulsion phase can be estimated only in allopolyploids. For autopolyploids, it is impractical to estimate meaningful linkages in repulsion because very large family sizes (>750) are required. For high-level polyploids of unknown genome constitution, the ratio between the number of detected repulsion versus coupling linkages may provide a crude measurement of preferential chromosome pairing, which can be used to distinguish allopolyploidy from autopolyploidy. To create a mapping population, one parent (P1) should have high heterozygosity to ensure a high frequency of SDRFs, and the second parent (P2) should have a low level of heterozygosity to increase the probability of detecting polymorphic fragments. This condition could be satisfied by choosing outcrossed hybrids as one parental type and inbreds, haploids, or doubled haploids as the other parental type.

High-resolution Mapping and Analysis of the Resistance Locus Rpi-abpt Against Phytophthora infestans in Potato

“…Band intensity was discarded to use AFLP markers as dominant markers and only simplex-inherited markers [single-dose restriction fragments, (SDRFs); Wu et al 1992] with a simplex trait allele for the detection of linkage in the coupling phase were included in the data analysis. The linkage group containing the resistance locus was determined by JoinMap 2.0 (Stam 1993) and marker order by Record (van Os et al 2000).…”

Linkage mapping in tetraploid willows: segregation of molecular markers and estimation of linkage phases support an allotetraploid structure for Salix alba × Salix fragilis interspecific hybrids

“…When the difference between coupling and repulsion phase marker combinations was not statistically significant, chromosome pairing was considered preferential. However, if the difference was significant, chromosome pairing was considered to be random (Wu et al, 1992). …”

“…Both the expected segregation ratios and linkage equations for SDMs linked in coupling are equivalent to those for diploids. The same holds for repulsion phase linkages in species with a preferential pairing, such as allopolyploids (Wu et al, 1992). The definition of the expected segregation ratios is more complicated in autopolyploids and relies on many factors, including the ploidy level, the chromosome pairing behaviour and the extent of double reduction (Wu et al, 1992).…”

“…Since willows have a high basic chromosome number (x ¼ 19), species with 2n ¼ 38 may be ancient polyploid derivatives (Stebbins, 1950;Lewis, 1980) that behave as functionally diploids (Aravanopoulos et al, 1993;Triest et al, 1998). A practical way to handle molecular marker data in polyploids is to treat each band as a marker allele of a single locus of a given genotype and to infer its allelic dose by studying the segregation ratio among progeny (Wu et al, 1992;Hackett et al, 1998;Ripol et al, 1999;Porceddu et al, 2002). A band present in a single dose (single-dose marker, SDM) in a tetraploid plant, for example, will be inherited by half of the gametes.…”

Effect of the parthenocarpy gene P1 and ploidy on fruit and bunch traits of plantain-banana hybrids

“…When dL<d<du or 4-du<d<4-dL the test is inconclusive. variation in polysomic polyploids, although methods and models have been proposed recently (Ortiz & Peloquin, 1992;Wu et al, 1992;Ortiz et al, 1993;Tai, 1994).…”