With less than 300 years of breeding, pedigrees for thousands of F. ananassa individuals have been recorded, albeit in disparate sources. To delve more deeply into the domestication history of cultivated strawberry, we assembled pedigree records from hundreds of sources and reconstructed the genealogy as deeply as possible. One of our initial motives for reconstructing the genealogy of cultivated strawberry was to identify historically important and genetically prominent ancestors of domesticated populations, in large part to guide the selection of individuals for whole-genome shotgun sequencing and DNA variant discovery, inform the development of single-nucleotide polymorphism genotyping platforms populated with octoploid genome-anchored subgenome-specific assays, and identify individuals for inclusion in genome-wide studies of biodiversity and population structure . The genetic relationships and genetic contributions of ancestors uncovered in the genealogy study described here guided the selection of individuals for downstream genomic studies that shed light on genetic variation and the genetic structure of domesticated populations worldwide . Our other early motive for reconstructing the genealogy of strawberry was to support the curation and stewardship of a historically and commercially important germplasm collection preserved at the University of California, Davis , plastic grow bag with accessions tracing to the early origins of the strawberry breeding program at the University of California, Berkeley , in the 1920s .
We sought to develop a complete picture of genetic relationships among living and extinct individuals in the California and worldwide populations, in part to assess how extinct individuals relate to living individuals preserved in public germplasm collections. Because 80% or more of the individuals we documented in the genealogy appear to be extinct, they could only be connected to living individuals through their pedigrees. One of the ways we explored ancestral interconnections between extinct and living individuals was through multivariate analyses of a combined pedigree–genomic relationship matrix estimated from genotyped and ungenotyped individuals . The holdings and history of the UCD Strawberry Germplasm Collection were shrouded in mystery when our study was initiated in 2015. The only individuals in the collection with pedigree records were publicly released and patented cultivars. The immediate challenge we faced in reconstructing the genealogy was the absence of pedigree records for 96% of the 1,287 accessions preserved in the collection, which is hereafter identified as the “California” population. To solve this problem, authenticate pedigrees, and fully reconstruct the genealogy of the California population, we applied an exclusion analysis in combination with high-density SNP genotyping . Here, we demonstrate the exceptional accuracy of diploid paternity analysis methods when applied to individuals in an allooctoploid organism genotyped with subgenome-specific SNPs on high-density arrays . Several thousand SNP markers common to the three arrays were integrated to develop a SNP profile database for the parentage analyses described here. SNPs on the 50-K and 850-K arrays are uniformly distributed across the octoploid genome and informative in octoploid populations worldwide . The 50-K SNP array harbors 1 SNP/16,200 bp, whereas the 850-K array harbors 1 SNP/953 bp, telomere-to-telomere across the 0.81-Gb octoploid genome.
The genealogies of domesticated plants, especially those with long-lived individuals, overlapping generations, and extensive migration and admixture, can be challenging to visualize and comprehend . We used Helium to visualize smaller targeted pedigrees; however, the strawberry pedigree networks we constructed and investigated were too large and mathematically complex to be effectively visualized and analyzed with Helium and other traditional hierarchical pedigree visualization approaches. Hierarchical methods often produce comprehensible insights and graphs when applied to pedigrees of individuals or small groups but yield exceedingly complex,labyrinthine graphs that are difficult to interpret when the genealogy contains a large number of individuals and lineages. We turned to social network analysis to explore alternative approaches to search for patterns and extract information from the complex genealogy of strawberry. The pedigree networks of plants and animals share many of the features of social networks with nodes connected to one another through edges relationships. We used SNA methods, in combination with classic population genetic methods, to analyze the genealogy and develop deeper insights into the domestication history of strawberry . SNA approaches have been applied in diverse fields of study but have apparently not been applied to the problem of analyzing and characterizing pedigree networks . With SNA, narrative data are translated into relational data and summary statistics and visualized as sociograms . Here, we report insights gained from genealogical studies of domesticated strawberry populations worldwide. Our studies shed light on the complex wild ancestry of F. ananassa, the diversity of founders of domesticated populations of cultivated strawberry that have emerged over the past 300 years, and genetic relationships among extinct and extant ancestors in demographically unique domesticated populations tracing to the earliest ancestors and inter specific hybrids .
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 outward facing barometer of progress in strawberry breeding. When translated across the past 200 years of breeding, 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, pe grow bag 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. Those nucleated the pedigree database we developed and were a catalyst for our study. 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. Another disadvantage of growing table grapes in subtropical areas is that high temperatures during ripening can inhibit anthocyanin biosynthesis in the berries from V. labrusca and hybrid cultivars . This results in inadequate fruit color, and thereby a decrease in market acceptance and the potential economic value of the commodity . The seedless table grape Selection 21, a new hybrid of V. vinifera × V. labrusca recently developed by the Grape Genetic Breeding Program of Embrapa Grape and Wine, Brazil, obtained from the cross of [Arkansas 1976 × ] × “BRS Linda,” is a clear example of a cultivar that lacks red color development when grown in subtropical regions. The plant growth regulator ethephon, an ethylene-releasing agent, has long been known to improve berry color when applied at véraison . More recently, the application of –cis-abscisic acid has also been shown to stimulate anthocyanin accumulation and thereby improve berry color . S-ABA appears to be more effective than ethephon in enhancing grape color and it has other potential benefits compared to ethephon, including a shorter postharvest interval, and an exemption from tolerance in most countries. The introduction of S-ABA as an active ingredient in a commercial plant growth regulator prompted many studies on V. vinifera cultivars under temperate climate conditions. Such studies have shown that the efficacy of S-ABA varies with the cultivar , the S-ABA concentration , the time of application and the environmental conditions . Studies have shown that exogenous application of S-ABA can significantly increase the activity of a wide range of genes involved in anthocyanin biosynthesis . Most of these studies tested the effects of a single application of S-ABA before or during véraison. However, studies of the effects of S-ABA several applications at different concentrations and timings following véraison are still needed to optimize the use of this plant growth regulator in table grape cultivation . In grapes, the anthocyanin biosynthesis pathway involves multiple steps that are controlled by MYB transcription factors, such as VvMYBA1 and VvMYBA2 . In red varieties, the VvMYBA1 gene is only expressed after véraison. Both VvMYBA1 and VvMYBA2 regulate anthocyanin biosynthesis during ripening by strictly controlling the expression of the canonical UDP-glucose:flavonoid 3-Oglucosyltransferase gene .