polymapR – linkage analysis and genetic map construction from F1 populations of outcrossing polyploids

MotivationPolyploid species carry more than two copies of each chromosome, a condition found in many of the world’s most important crops. Genetic mapping in polyploids is more complex than in diploid species, resulting in a lack of available software tools. These are needed if we are to realise all the opportunities offered by modern genotyping platforms for genetic research and breeding in polyploid crops.ResultspolymapR is an R package for genetic linkage analysis and integrated genetic map construction from bi-parental populations of outcrossing autopolyploids. It can currently analyse triploid, tetraploid and hexaploid marker datasets and is applicable to various crops including potato, leek, alfalfa, blueberry, chrysanthemum, sweet potato or kiwifruit. It can detect, estimate and correct for preferential chromosome pairing, and has been tested on high-density marker datasets from potato, rose and chrysanthemum, generating high-density integrated linkage maps in all of these crops.Availability and ImplementationpolymapR is freely available under the general public license from the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/packages=polymapR.ContactChris Maliepaard [email protected] or Roeland E. Voorrips [email protected]

Construction of a genetic linkage map for Saccharum officinarum incorporating both simplex and duplex markers to increase genome coverage

Saccharum officinarum L. is an octoploid with 80 chromosomes and a basic chromosome number of x = 10. It has high stem sucrose and contributes 80% of the chromosomes to the interspecific sugarcane cultivars that are grown commercially for sucrose. A genetic linkage map was developed for S. officinarum (clone IJ76-514) using a segregating population generated from a cross between Q165 (a commercial sugarcane cultivar) and IJ76-514. In total, 40 AFLP and 72 SSR primer pairs were screened across the population, revealing 595 polymorphic bands inherited from IJ76-514. These 595 markers displayed a frequency distribution different from all other sugarcane genetic maps produced, with only 40% being simplex markers (segregated 1:1). Of these 240 simplex markers, 178 were distributed on 47 linkage groups (LGs) and 62 remained unlinked. With the addition of 234 duplex markers and 80 biparental simplex markers (segregating 3:1), 534 markers formed 123 LGs. Using the multi-allelic SSR markers, repulsion phase linkage, and alignment with the Q165 linkage map, 105 of the 123 LGs could be grouped into 10 homology groups (HGs). These 10 HGs were further assigned to the 8 HGs observed in cultivated sugarcane and S. spontaneum . Analysis of repulsion phase linkage indicated that IJ76-514 is neither a complete autopolyploid nor an allopolyploid. Detection of 28 repulsion linkages that occurred between 6 pairs of LGs located in 4 HGs suggested the occurrence of limited preferential chromosome pairing in this species.

Chromosome Homology in Tetraploid Southern Highbush × Vaccinium elliottii Hybrids

A yellow-leaf seedling marker, r, was used to determine if there was preferential chromosome pairing in a group of tetraploid southern highbush blueberry hybrids. Plants with four copies of r (no copies of R) fail to develop anthocyanins, and cotyledons, hypocotyls, leaves, stems, and other vegetative tissues have a bright yellow-green color. In the hybrids that were studied, two genomes were from the diploid wild species, V. elliottii Chapman, and both carried the recessive marker r. The other two genomes were from southern highbush cultivars and both carried the dominant wildtype allele, R. When RRrr hybrids were intercrossed or crossed to rrrr yellow-leaf plants, the number of yellowleaf rrrr seedlings obtained usually equalled or exceeded the number predicted from nonpreferential chromosome pairing. Since rr gametes can only be produced by RRrr plants when R and r chromosomes pair at Meiosis I, there was no evidence that the chromosomes derived from V. elliottii were pairing at a higher-than-random rate.

INTERSPECIFIC CROSSES INVOLVING ALFALFA. IV. Medicago glomerata × M. sativa with reference to M. prostrata

A good seed set was obtained from crosses of Medicago glomerata Balb. with M. sativa L. There was no evidence of a preferential chromosome pairing effect on segregation for floral anthocyanin. From an analysis of different M. glomerata × M. sativa crosses four factors were found to be involved in anthocyanin production. About 90% of the cells showed normal chromosome behavior during meiosis. Taxonomically, M. glomerata stands somewhat apart from the M. sativa — falcata complex, as indicated by a lower seed set from intercrossed F1's, and by somewhat higher numbers of meiotic irregularities in the F1 plants. With these and other morphological differences M. glomerata is considered as a separate species. When hybridized with M. prostrata Jacq., M. glomerata responded in a similar manner to that of M. sativa. The weight of seeds produced by M. glomerata plants was approximately the same, whether fertilized by M. glomerata or by M. sativa pollen. There is a somewhat greater affinity between M. glomerata and M. prostrata than between M. sativa and M. prostrate; M. prostrata plants fertilized by M. glomerata pollen had better seed development than those fertilized by M. sativa.