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

Abstract

Salix albaÀSalix fragilis complex includes closely related dioecious polyploid species, which are obligate outcrossers. Natural populations of these willows and their hybrids are represented by a mixture of highly heterozygous genotypes sharing a common gene pool. Since nothing is known about their genomic constitution, tetraploidy (2n ¼ 4x ¼ 76) in willow species makes basic and applied genetic studies difficult. We have used a two-way pseudotestcross strategy and singledose markers (SDMs) to construct the first linkage maps for both pistillate and staminate willows. A total of 242 amplified fragment length polymorphisms (AFLPs) and 50 selective amplifications of microsatellite polymorphic loci (SAMPL) markers, which showed 1:1 segregation in the F 1 mapping populations, were used in linkage analysis. In S. alba, 73 maternal and 48 paternal SDMs were mapped to 19 and 16 linkage groups covering 708 and 339 cM, respectively. In S. fragilis, 13 maternal and 33 paternal SDMs were mapped in six and 14 linkage groups covering 98 and 321 cM, respectively. For most cosegregation groups, a comparable number of markers linked in coupling and repulsion was identified. This finding suggests that most of chromosomes pair preferentially as occurs in allotetraploid species exhibiting disomic inheritance. The detection of 10 pairs of marker alleles from single parents showing codominant inheritance strengthens this hypothesis. The fact that, of the 1122 marker loci identified in the two male and female parents, the vast majority (77.5%) were polymorphic and as few as 22.5% were shared between parental species highlight that S. alba and S. fragilis genotypes are differentiated. The highly difference between S. alba-and S. fragilis-specific markers found in both parental combinations (on average, 65.3 vs 34.7%, respectively) supports the (phylogenetic) hypothesis that S. fragilis is derived from S. alba-like progenitors.

Clones Identification and Genetic Characterization of Garnacha Grapevine by Means of Different PCR-Derived Marker Systems

“…Selective amplification of microsatellite polymorphic loci (SAMPL) markers analysis was performed using a procedure identical to that adopted for AFLP reported above, except for the second amplification, where the PCR was performed with the Cy5 labelled Asl or As2 adjacentmicrosatellite primer and a standard Msel primer with three selective nucleotides [47,48]. The cycling conditions were 2 cycles of 45 s at 94°C, 30 s at 56°C, 1 min at 72°C, 13 cycles of 30 s at 94°C, 30 s at 55.3°C and 1 min at 72°C with a touch-down profile for the annealing temperature (13 cycles with -0.7°C/cycle) and 18 cycles of 30 s at 94°C, 30 s at 48°C and 1 min at 72°C; finally by an extension cycle of 5 min at 72°C [39].…”

Genetic Segregation and Genomic Hybridization Patterns Support an Allotetraploid Structure and Disomic Inheritance for Salix Species

“…Morphology indicates that pure species of the Salix alba L. (white willow)-Salix fragilis L. (crack willow) complex and their natural hybrids form a polyploid complex of closely related willows [11][12][13][14].…”

Constructing Genetic Linkage Maps Under a Tetrasomic Model

“…In addition to the aforementioned complexities (i-iii), challenges in modeling these PCRbased genetic markers involve (iv) occurrence of null alleles due to experimental failure to identify the presence of some alleles and (v) one phenotype representing several genotypes. Linkage analyses of autopolyploids in the current literature have been based either on the use of single-dose (simplex) dominant markers (e.g., AFLPs and RAPDs) that segregate in a simple 1:1 ratio in mapping populations (Wu et al 1992;Meyer et al 1998;Brouwer and Osborn 1999;Barcaccia et al 2003) or on assuming solely random bivalent pairing among homologous chromosomes (Ripol et al 1999;Hackett et al 2001;Luo et al 2001;Bradshaw et al 2004;Cao et al 2005). These have effectively avoided the analytical complexities but at the same time ignored some essential features of the problems.…”