For ancestors, GC was iteratively estimated by MK between each ancestor and cultivars within a focal population, starting with the ancestor with the largest MK estimated from A, deleting that ancestor, re-estimating the coancestry matrix , selecting the ancestor with the largest MK estimated from the pruned coancestry matrix , deleting that ancestor, re-estimating the coancestry matrix, and repeating until every ancestor had been dropped. We compiled GC, B, and do estimates for every founder and non-founder in the pedigree database . We identified four F. chiloensis, five F. virginiana, and 40 F. ananassa founders in the genealogy of the California population . Cumulative GC estimates for the California population were 1.8% for F. chiloensis, 12.7% for F. virginiana, and 85.5% for F. ananassa founders. Four of the nine wild octoploid founders of the California population were founders of the historic Ettersburg population that supplied genetic diversity for private and public sector breeding programs in California . The wild octoploid founders with the largest GCs were three F. virginiana ecotypes: “New Jersey Scarlet” , “Hudson Bay” , and “Wasatch” . Wasatch is the F. virginiana subsp. glauca donor of the PERPETUAL FLOWERING mutation that Bringhurst et al. transferred into F. ananassa . The Wasatch ecotype appears in the genetic background of every day-neutral cultivar developed at the UCD.Similarly, we identified 26 F. chiloensis, 24 F. virginiana,plant pot with drainage and 490 F. ananassa founders in the genealogy of the Cosmopolitan population . Cumulative GC estimates for the Cosmopolitan population were 4.6% for F. chiloensis, 14.1% for F. virginiana, 79.9% for F. ananassa, and 1.4% for other founders.
Similar to what we found for the California population, the wild octoploid founders with the largest GCs were “New Jersey Scarlet” and “Hudson Bay” . The next largest GC was made by FC_071 , an F. chiloensis ecotype of unknown origin found in the pedigrees of Madame Moutot, Sharpless, Royal Sovereign, and other influential early cultivars . A significant fraction of the alleles found in F. ananassa populations have flowed through a comparatively small number of common ancestors, each of which have contributed unequally to standing genetic variation . The most important ancestors are described as “stars” in the lexicon of SNA, and are either locally or globally central . Globally central individuals reside in the upper-right quadrant of the B do distribution , where B is the mean of B and do is the mean of do—8.7-8.9% of the ancestors that were classified as globally central . Locally central individuals reside in the upperleft quadrant of the B do distribution —11.8- 12.1% of the ancestors were classified as locally central . “Tufts,” “Lassen,” “Nich Ohmer,” “Howard 17,” and “Fairfax” were among the biggest stars, along with several other iconic, mostly heirloom cultivars, and all were either locally or globally central . Stars are “gatekeepers” that have numerous descendants , transmitted a disproportionate fraction of the alleles found in a population , have the largest number of interconnections in the pedigree, and are visible in sociograms as nodes with radiating pinwheel-shaped patterns of lines . Several of the latter are visible in the sociograms we developed for the California and Cosmopolitan populations. Stars have the largest nodes in the sociograms . We estimated and compiled GC statistics for every ancestor in the California and Cosmopolitan populations . The twenty-most prominent and historically important ancestors of the California and Cosmopolitan populations are shown in Table 2.
They include several iconic and well known heirloom and modern cultivars, e.g., “Tioga,” “Douglas,” and “Royal Sovereign” , in addition to “unreleased” germplasm accessions preserved in the UCD Strawberry Germplasm Collection, e.g., 65C065P601 . The latter is the oldest living descendant of the aforementioned F. virginiana subsp. glauca “Wasatch” ecotype collected by Royce S. Bringhurst from the Wasatch Mountains, Little Cottonwood Canyon, Utah . The “Wasatch” ecotype is a founder of every day-neutral cultivar in the California population and many day-neutral cultivars in the Cosmopolitan population with alleles flowing through 65C065P601 and the UCD cultivar “Selva” . GC statistics were ordered from largest to smallest and progressively summed to calculate the cumulative GCs of ancestors and the number of ancestors needed to explain p% of the genetic variation in a focal population, where p ranges from 0 to 100% . The parameter n100 estimates the number of ancestors needed to account for 100% of the genetic variation among k cultivars in a focal population . n100 estimates were 153 for the California population and 3,240 for the Cosmopolitan population. The latter number was significantly larger than the number for the California population because the Cosmopolitan population includes pedigrees for 2,499 cultivars developed worldwide, whereas the California population includes pedigrees for 69 UCDcultivars only . Within European countries, n100 ranged from 25 for Belgium to 342 for England . Within the United States, n100 ranged from a minimum of 367 for the southern region to a maximum of 444 for western and northeastern regions. Predictably, np increased at a decreasing rate as the number of GC-ranked ancestors increased . Cumulative GC estimates increased as nonlinear diminishing-return functions of the number of ancestors .
The slopes were initially steep because a fairly small number of ancestors accounted for a large fraction of the genetic variation within a particular focal population. Across continents, regions, and countries, eight to 112 ancestors accounted for 50% of the allelic variation within focal populations . The differences in np estimates were partly a function of the number of cultivars within each focal population. When np was expressed as a function of k, we found that the proportion of ancestors needed to explain p% of the allelic variation in a focal population was strikingly similar across continents, regions, and countries, e.g., the Western US population, which had the largest n100 estimate , fell squarely in the middle when expressed as a function of k . Breeding speed and pedigree-informed predictive breeding in cultivated strawberry SNAs of the pedigree networks shed light on the speed of breeding and changes in the speed of breeding over the past 200 years in strawberry . We retraced the ancestry of every cultivar through nodes and edges in the sociograms . The year of origin was known for 71% of the individuals. These edges yielded robust estimates of the mean selection cycle length in years . S was calculated from thousands of directed acyclic graphs, which are unidirectional paths traced from cultivars back through descendants to founders . Collectively, cultivars in the California population visited 27,058 PO edges, whereas cultivars in the Cosmopolitan population visited 155,487 PO edges. The selection cycle length means and distributions over the past 200 years were strikingly similar across continents, regions, and countries—S was 16.9 years/generation for the California population and 16.0 years/generation for the Cosmopolitan population . These extraordinarily long selection cycle lengths are more typical of a long-lived woody perennial than of a fast cycling annual ; however, the speed of breeding has steadily increased over time . By 2000, S had decreased to six years/generation in the California population and 10 years/generation in the Cosmopolitan population . The genealogy does not account for lineages underlying what must have been millions of hybrid progeny screened in breeding programs worldwide; e.g., Johnson alone reported screening 600,000 progeny over 34 years at Driscoll’s . Cultivars are, nevertheless, an accurate barometer of global breeding activity and the only outwardfacing barometer of progress in strawberry breeding. When translated across the past 200 years of breeding,pot with drianage holes our selection cycle length estimates imply that the 2,656 cultivars in the genealogy of cultivated strawberry have emerged from the mathematical equivalent of only 12.9 cycles of selection . Even though offspring from 250 years of crosses have undoubtedly been screened worldwide since 1770, 15.5 years has elapsed on average between parents and offspring throughout the history of strawberry breeding . Because genetic gains are affected by selection cycle lengths, and faster generation times normally translate into greater genetic gains and an increase in the number of recombination events per unit of time , our analyses suggest that genetic gains can be broadly increased in strawberry by shortening selection cycle lengths. Genome-informed breeding and speed breeding are both geared towards that goal and have the potential to shorten selection cycle lengths and increase genetic gains .
We reconstructed the genealogy of strawberry to inform the curation of a historically important germplasm collection, forensically identify the parents of individuals without pedigree records, authenticate the parents of individuals with pedigree records, shed light on the domestication history of strawberry, and retrospectively examine where we have been and how we got there. The reconstruction was greatly facilitated by the availability of outstanding SNP genotyping platforms , the development of an extensive DNA profile database to complement the pedigree database , and the application of robust and highly accurate diploid exclusion analysis methods for parent identification and pedigree authentication. We provided an open-source R code to support future parentage analyses in agricultural species. Our backward-facing genealogy study, in retrospect, yielded unexpected insights about the complex hybrid ancestry and breeding history of cultivated strawberry that should inspire future generations and guide where we should go from here. Our critical examination of historical selection cycle lengths was meant to be provocative and perhaps inspire the implementation of strategies for increasing breeding speed and accelerating the improvement of strawberry. We suspect that improvements can be achieved, at least in part, through changes in breeding schemes and the application of pedigree-informed predictive breeding methods. The open-source pedigree database we compiled should find broad utility in predictive breeding schemes and can be easily expanded and modified for specific breeding problems, other populations, and future analyses. Because of the depth and completeness of the pedigree records commonly available in strawberry, pedigree best linear unbiased prediction has the potential to increase genetic gains and enhance selection decisions, especially when combined with genomic prediction . The pedigree database we assembled will facilitate the application of pedigree-BLUP and identity-by-descent prediction of alleles and haplotypes , in addition to providing a solid foundation for expanding the genealogy over time.We are grateful to Clint Pumphrey, the manuscript curator of the special collections and archives of the Merrill-Cazier Library at Utah State University . Clint assisted the first author with acquiring and researching the laboratory notebooks and other records of Royce S. Bringhurst , a former faculty member and strawberry breeder at the UCD . The documents and photos associated with the collection yielded extensive pedigree records that were crucial for reconstructing the genealogy of the UCD Strawberry Breeding Program. We are equally grateful to Phillip Stewart, a strawberry breeder at Driscoll’s , for sharing copies of the UCB, pedigree records of Harold E. Thomas , a former faculty member and strawberry breeder at UCB from 1927 to 1945. Those pedigree records greatly increased the completeness and depth of the database for the early years of the University of California Strawberry Breeding Program. The authors thank Thomas Sjulin, a former strawberry breeder at Driscoll’s , for sharing the public pedigree records he assembled over his career. SJK and GSC thank Robert Kerner for the computer forensic analyses that recovered several hundred pedigree records for UCD individuals from an obsolete electronic database, thus preventing the loss of those records for perpetuity. They were critical for integrating the UCD genealogy with the global genealogy for cultivated strawberry. SJK especially thanks Rachel Krevans, Matthew Chivvis, Jake Ewert, and Wesley Overson for their integrity, friendship, and steadfast support.Table grapes have become an important fresh commodity in Brazil for both internal market and exportation. Over the period of 2000–2016, Brazil presented an increase of ∼150% in table grape production, reaching around 970,000 MT in 2016 . The northern region of Paraná state is one of the main areas of table grape production. The mild winter and subtropical conditions of this region permit two crops of grapes per year, which allow Brazilian growers to time their production to coincide with market windows of other countries and compete for more advantageous prices. However, in these subtropical regions, berry ripening and harvest often occur during the rainy season, which is not ideal for Vitis vinifera cultivars because excess rain and moisture compromise the overall quality of the berries . Therefore, Brazilian table grape production is starting to incorporate American and/or hybrid grape cultivars that are better adapted to warm and rainy climates.