Evidence of epistatic suppression of repeat fruiting in cultivated strawberry

BACKGROUND

Consumers purchase fresh strawberries all year long. Extending the fruiting season for new strawberry cultivars is a common breeding goal. Understanding the inheritance of repeat fruiting is key to improving breeding efficiency. Several independent research groups using multiple genotypes and analytic approaches have all identified a single genomic region in strawberry associated with repeat fruiting. Markers mapped to this region were used to evaluate breeding parents from the United States Department of Agriculture - Agricultural Research Service (USDA-ARS) strawberry breeding program at Beltsville, Maryland.

RESULTS

Markers mapped to repeat fruiting identified once-fruiting genotypes but not repeat-fruiting genotypes. Eleven of twenty-three breeding parents with repeat-fruiting marker profiles were actually once fruiting, indicating at least one additional locus acting epistatically to suppress repeat fruiting. Family segregation ratios could not be predicted reliably by the combined use of parental phenotypes and marker profiles, when using a single-gene model. Expected segregation ratios were calculated for all phenotypic and marker-profile combinations possible from the mapped locus combined with a hypothetical dominant or recessive suppressor locus. Segregation ratios specific to an epistatic suppressor acting on the mapped locus were observed in four families. The segregation ratios for two families were best explained by a dominant suppressor acting on the mapped locus, and, for the other two, by a recessive suppressor. Not all of the observed ratios could be explained by one model or the other, and when multiple families with a common parent were compared, there was no predicted genotype for the common parent that would lead to all of the observed segregation ratios.

CONCLUSIONS

Considering all lines of evidence in this study and others, repeat-fruiting in commercial strawberry is controlled primarily by a dominant allele at a single locus, previously mapped by multiple groups. At least two additional genes, one dominant and one recessive, exist that act epistatically to suppress repeat fruiting. Environmental effects and/or incomplete penetrance likely affect phenotype through the suppressor loci, rather than the primary mapped locus. One of the dominant suppressors acts only in the first year, the year the plant is germinated from seed, and not after the plant has experienced a winter.

Genetic map of the primocane-fruiting and thornless traits of tetraploid blackberry

Blackberry primocane fruiting, fruiting on first-year canes, has the potential to expand blackberry production both seasonally and geographically. The incorporation of the primocane-fruiting trait into cultivars with desirable horticultural attributes is challenging due to its recessive nature and tetrasomic inheritance. Molecular marker-assisted selection has high potential to facilitate incorporation, because breeders already use morphological marker-assisted selection of seedlings without marginal cotyledonary hairs to identify progeny that will be thornless when mature. The development of a genetic linkage map with these two traits is the first step to utilizing molecular markers in breeding for thornless primocane-fruiting blackberry cultivars. A full-sib family segregating for thornlessness and primocane fruiting, from a cross between 'APF-12' and 'Arapaho', was used to construct the first genetic map of tetraploid blackberry. Segregation patterns of several dominant markers and the two phenotypic traits fit those expected uniquely with tetrasomic inheritance (e.g., 5:1, 11:1 and 35:1). Some loci showed significant double reduction frequencies, but genotypes that could have originated only from double reduction were not found. The map consists of seven linkage groups (LG) in each parent, consistent with the basic number of chromosomes (2n = 4x = 28). Naming of LG1-LG6 followed that of the recently revised system for raspberry using SSR markers in common between blackberry and raspberry, and LG7 was tentatively defined by default. The loci controlling primocane fruiting and thornlessness were not linked to each other; thornless/thorny, the S Locus, was mapped on LG4, and the primocane-/floricane-fruiting locus, named in this work the F Locus, on LG7.

Construction of black (Rubus occidentalis) and red (R. idaeus) raspberry linkage maps and their comparison to the genomes of strawberry, apple, and peach

The genus Rubus belongs to the Rosaceae and is comprised of 600-800 species distributed world-wide. To date, genetic maps of the genus consist largely of non-transferable markers such as amplified fragment length polymorphisms. An F(1) population developed from a cross between an advanced breeding selection of Rubus occidentalis (96395S1) and R. idaeus 'Latham' was used to construct a new genetic map consisting of DNA sequence-based markers. The genetic linkage maps presented here are constructed of 131 markers on at least one of the two parental maps. The majority of the markers are orthologous, including 14 Rosaceae conserved orthologous set markers, and 60 new gene-based markers developed for raspberry. Thirty-four published raspberry simple sequence repeat markers were used to align the new maps to published raspberry maps. The 96395S1 genetic map consists of six linkage groups (LG) and covers 309 cM with an average of 10 cM between markers; the 'Latham' genetic map consists of seven LG and covers 561 cM with an average of 5 cM between markers. We used BLAST analysis to align the orthologous sequences used to design primer pairs for Rubus genetic mapping with the genome sequences of Fragaria vesca 'Hawaii 4', Malus × domestica 'Golden Delicious', and Prunus 'Lovell'. The alignment of the orthologous markers designed here suggests that the genomes of Rubus and Fragaria have a high degree of synteny and that synteny decreases with phylogenetic distance. Our results give unprecedented insights into the genome evolution of raspberry from the putative ancestral genome of the single ancestor common to Rosaceae.

Genetic mapping of sex determination in a wild strawberry, Fragaria virginiana, reveals earliest form of sex chromosome

The evolution of separate sexes (dioecy) from hermaphroditism is one of the major evolutionary transitions in plants, and this transition can be accompanied by the development of sex chromosomes. Studies in species with intermediate sexual systems are providing unprecedented insight into the initial stages of sex chromosome evolution. Here, we describe the genetic mechanism of sex determination in the octoploid, subdioecious wild strawberry, Fragaria virginiana Mill., based on a whole-genome simple sequence repeat (SSR)-based genetic map and on mapping sex determination as two qualitative traits, male and female function. The resultant total map length is 2373 cM and includes 212 markers on 42 linkage groups (mean marker spacing: 14 cM). We estimated that approximately 70 and 90% of the total F. virginiana genetic map resides within 10 and 20 cM of a marker on this map, respectively. Both sex expression traits mapped to the same linkage group, separated by approximately 6 cM, along with two SSR markers. Together, our phenotypic and genetic mapping results support a model of gender determination in subdioecious F. virginiana with at least two linked loci (or gene regions) with major effects. Reconstruction of parental genotypes at these loci reveals that both female and hermaphrodite heterogamety exist in this species. Evidence of recombination between the sex-determining loci, an important hallmark of incipient sex chromosomes, suggest that F. virginiana is an example of the youngest sex chromosome in plants and thus a novel model system for the study of sex chromosome evolution.

High variability and disomic segregation of microsatellites in the octoploid Fragaria virginiana Mill. (Rosaceae)

The objectives of the present study were to develop microsatellite markers for the wild strawberry, Fragaria virginiana, to evaluate segregation patterns of microsatellite alleles in this octoploid species, and assess genetic variability at microsatellite loci in a wild population. A genomic library was screened for microsatellite repeats and several PCR primers were designed and tested. We also tested the use of heterologous primers and found that F. virginiana primers amplified products in cultivated strawberry, Fragaria x ananassa Duch. and Fragaria chiloensis. Similarly, microsatellite loci developed from cultivated strawberry also successfully amplified F. virginiana loci. We investigated four microsatellite loci in detail, three developed from F. virginiana and one from cultivated strawberry. A survey of 100 individuals from a population of F. virginiana in Pennsylvania demonstrated high heterozygosities (H(e) or gene diversity ranged from 0.80 to 0.88 per locus) and allelic diversity (12-17 alleles per locus), but individual plants had no more than two alleles per locus. Segregation patterns in parents and progeny of two controlled crosses at these four loci were consistent with disomic Mendelian inheritance. Together these findings suggest that the genome of F. virginiana is "highly diploidized" and at least a subset of microsatellite loci can be treated as codominant, diploid markers. Significant heterozygote deficiencies were found at three of the four loci for hermaphroditic individuals but for only one locus among females in this gynodioecious species.

Physical mapping of resistant and susceptible soybean genomes near the soybean cyst nematode resistance gene Rhg4

The soybean cyst nematode (SCN), Heterodera glycines Ichinohe, is the foremost pest of soybean (Glycine max L. Merr.). The rhg1 allele on linkage group (LG) G and the Rhg4 allele on LG A2 are important in conditioning resistance. Markers closely linked to the Rhg4 locus were used previously to screen a library of bacterial artificial chromosome (BAC) clones from susceptible 'Williams 82' and identified a single 150-kb BAC, Gm_ISb001_056_G02 (56G2). End-sequenced subclones positioned onto a restriction map provided landmarks for identifying the corresponding region from a BAC library from accession PI 437654 with broad resistance to SCN. Seventy-three PI 437654 BACs were assigned to contigs based upon HindIII restriction fragment profiles. Four contigs represented the PI 437654 counterpart of the 'Williams 82' BAC, with PCR assays connecting these contigs. Some of the markers on the PI 437654 contigs are separated by a greater physical distance than in the 'Williams 82' BAC and some primers amplify bands from BACs in the mid-portion of the connected PI 437654 BAC contigs that are not amplified from the 'Williams 82' BAC. These observations suggest that there is an insertion in the PI 437654 genome relative to the 'Williams 82' genome in the Rhg4 region.

A testcross procedure for selecting exotic strains to improve pure-line cultivars in predominantly self-fertilizing species

Methods for identifying germplasm carrying alleles with the potential to improve a particular single-cross hybrid have been proposed and discussed in recent years. There is a need for similar methods to be used in breeding crops for which pure-line cultivars, rather than hybrids, are the goal. The objective of this research was to develop a method to identify germplasm lines with the potential to contribute favorable alleles not present in a specified pure line or set of pure lines. Given a set of adapted pure lines (A 1, A 2 ..., A m) to be improved and a set of germplasm lines (P 1 P 2 ..., P f), the procedure consists of producing all f x m possible hybrids and evaluating them along with the parents. The testcross statistic T ij is defined by T ij=γ(F ij-A j)+(1-γ) (F ij-P i), where A j, P i, and F ij represent the performance of thej (th) adapted line, the i (th) germplasm line, and their hybrid, respectively. The statistic [Formula: see text] is the mean value of T ij over all adapted parents A j. If γ=(1/2)(1+d'), where d' = the mean degree of dominance, then T ij measures the potential for alleles from P i to improve A j and [Formula: see text] measures the potential for alleles from P i to improve the set A 1, A 2 ..., A m. Use of data on soybean and peanut hybrids published by other researchers suggests that the value assumed for d' has little effect on the P i chosen. The ability of the T ij and [Formula: see text] statistics to identify germplasm strains carrying rare favorable alleles should be assessed in empirical studies.