Pedigrees of apple (Malus ×domestica Borkh.) cultivars were used to study worldwide genetic diversity among clones used in modern apple breeding. The most frequent founding clones were `Cox's Orange Pippin', `Golden Delicious', `Red Delicious', `Jonathan', and `McIntosh'. Coefficients of coancestry between 50 mainstream cultivars and these clones averaged 0.03, 0.12, 0.07, 0.06, and 0.02, respectively, but they were frequently as high as 0.25 with certain pairings. Among a group of 27 cultivars carrying the Vf gene for scab resistance, coefficients of coancestry with the five founding clones were of the same order. Although few of the cultivars sampled were substantially inbred, inbreeding could reach serious levels in their future offspring if current breeding practices are continued. The status effective number was 8 for the mainstream group and 7 for the Vf-carrier clones. This indicates clearly that apple breeders are operating with a population of greatly reduced genetic diversity. Careful consideration of pedigrees and increased size of the genetic base are needed in future apple breeding strategies.
Dominique A.M. Noiton and Peter A. Alspach
Ann Marie Connor, Chad E. Finn, and Peter A. Alspach
Antioxidant compounds absorbed from our diet are thought to have a role in preventing chronic diseases that result from oxidative damage. Berry fruit have high levels of antioxidants, and further increases in antioxidant activity (AA) might be possible through breeding. We determined the AA, total phenolic content (TPH), and fruit weight in 16 blackberry and hybridberry (Rubus L.) cultivars harvested in New Zealand and Oregon in 2002 and 2003, to assess genetic and environmental variation. Both AA and TPH varied significantly between years within location, but not among cultivars or between locations per se. However, cultivar interactions with both location and year within location contributed to variation in both variates. In contrast, both cultivar and location contributed to variation in fruit weight, but years within location did not. However, the cultivar × year within location interaction was significant for this trait. Variance component distributions confirmed that cultivar and location effects together contributed little (<20%) to the total variation in either AA or TPH, while cultivar × environment interactions accounted for >50% of total variation in these traits. Cultivar and location effects together contributed ≈70% of the total variation observed in fruit weight. Phenotypic correlations were significant between AA and fruit weight (r = -0.44), and between TPH and fruit weight (r = -0.51). When adjusted for fruit weight, analyses for AA and TPH demonstrated that cultivar effects approached significance (P = 0.06) and accounted for ≈25% of total variance, while location effects accounted for none. Although the cultivars in this study had diverse interspecific backgrounds, utilization of various Rubus species in blackberry and hybridberry breeding is not uncommon, and our results demonstrating significant cultivar × environment interaction for AA and TPH should be applicable to breeding for high AA genotypes.
M. Joseph Stephens, Peter A. Alspach, Ron A. Beatson, Chris Winefield, and Emily J. Buck
The Pacific northwestern (PNW) region of the United States is well known for production of machine-harvested red raspberries (Rubus idaeus) for process markets. The cultivar Meeker, developed in the 1960s, is well suited to this area and for machine-harvesting, but it is susceptible to raspberry bushy dwarf virus and root rot caused by Phytophthora rubi. Despite the efforts of several breeding programs, ‘Meeker’ is still the predominant cultivar for commercial production in the PNW. One of the major difficulties with breeding new berry fruit cultivars is the time-consuming nature of collecting fruit yield and quality data on large seedling populations. For fruit yield, visual scoring assessment methods are commonly used for seedling populations, but these may be poor predictors of yield. Consequently, visual scores for yield can result in less genetic improvement and thus can adversely affect successful cultivar development. Total yield measured by hand-harvesting is labor-intensive and does not assess machine-harvestability, but machine-harvesting is not practical to measure on individual plants. In this study we set out to see if we could bulk machine-harvest full-sib family plots for among-family selection and use yield component data on individuals within the plots for within-family selection. Using best linear unbiased predictors, we estimated machine-harvest yield breeding values for our individual seedlings and found higher genetic gain per generation using estimated individual machine-harvest breeding values (7.6%) than using hand-harvested breeding values (6.5%). Implications for breeding machine-harvest red raspberries are discussed.
M. Joseph Stephens, Peter A. Alspach, Ron A. Beatson, Chris Winefield, and Emily J. Buck
For most small fruit-breeding programs, high yield is a key objective and breeders face a number of challenges breeding for high yield, including interaction of environmental influences and the high cost of yield measurements. Red raspberry (Rubus idaeus) yield is determined by a number of yield components (YC), including cane number, cane length, number of fruiting laterals, fruit numbers, and fruit size. The ultimate goal for breeders would be to be able to select for high-yield genotypes using key YC as early in the life of the plant as possible. In this study we set out to determine how individual components of yield are inherited, determine which components contribute the most to total yield, and investigate whether it is possible using key components to make selections for high-yielding genotypes on 1- and 2-year-old plants. We estimated variance components, heritabilities, phenotypic and genotypic correlations, and breeding values for yield and YC from 1008 genotypes based on 85 families derived from 45 parents harvested over three seasons in Washington state. Narrow-sense heritability estimates varied from moderately low [0.2 for number of canes (NCAN)] to moderately high [0.69 for berry weight (BWT)]. In general, all YCs were positively correlated with total yield (TYLD). The highest genetic correlation with TYLD was found for BWT (0.8), followed by cane length (CLEN) (0.54) and number of fruit per lateral (NFRT) (0.5). NCAN had the lowest genetic correlation with TYLD (–0.03). Genotype × year (G×Y) interaction was higher for some YCs than others. Berry weight, lateral length (LLEN), and NFRT were found to be the most stable overall seasons and the interaction was higher between the first and second years than between the second and third years of the study. To determine the most important YC, we calculated the correlations between the product of all combinations of subsets of the YC breeding values and TYLD. Berry weight, CLEN, and cane diameter (CDIA) were found to be the most important for 2009, 2010, and 2011, respectively. The two most important YCs were LLEN and BWT and this was consistent overall seasons. We demonstrate that it is possible to select high-yielding genotypes by measuring key components such as LLEN, CLEN, and BWT in the first and second fruiting seasons.
M. Joseph Stephens, Peter A. Alspach, Ron A. Beatson, Chris Winefield, and Emily J. Buck
New commercial red raspberry (Rubus idaeus) cultivars suited to machine-harvesting and processing markets need to be high-yielding and have good fruit quality attributes, including fruit firmness, sugar content, acidity, flavor, and health properties. Combining many traits in one genotype is a challenge for breeders, especially for traits negatively correlated with yield. Despite its potential, the use of multiple-trait selection through selection indices has had limited application in fruit breeding. In this study, we estimated variance components, heritabilities, phenotypic and genetic correlations and breeding values for total yield (TYLD), harvest span, mid-harvest day and fruit quality traits, firmness (FIRM), soluble solids (SS), acidity (ACID), total anthocyanins (TACY), and total ellagitannins (TELG) from 1008 seedling genotypes based on 85 families derived from 45 parents harvested over three seasons in Washington state. Narrow-sense heritability estimates ranged from moderately low (0.22 for TYLD) to moderately high (0.73 for SS). All traits measured had positive genetic correlations with TYLD except for ACID (–0.35) and TACY (–0.28). Genotype × year (G×Y) interaction was high for TYLD and low for fruit quality attributes FIRM, SS, ACID, TACY, and TELG, and interactions were higher between the first (2009) and second (2010) seasons than between the second (2010) and third (2011) seasons. Using economic weights and breeding values derived from multivariate analysis for TYLD, FIRM, SS, and TACY, we constructed a selection index designed to assist with multiple-trait selection for population improvement and the development of commercial raspberry cultivars.
M. Joseph Stephens, Jessica Scalzo, Peter A. Alspach, Ron A. Beatson, and Ann Marie Connor
Breeding for high yield is a major objective of most small fruit breeding programs worldwide. In recent years, research associated with health benefits of berry fruit has resulted in some breeding programs looking for material with improved health properties with the goal of incorporating these into genotypes with high yield and other favorable agronomic characters. In this study, we estimated variance components, heritabilities, and phenotypic and genotypic correlations for yield components and phytochemicals [total phenolics (TPH), antioxidant activity (FRAP), and total anthocyanins (TACY)] from 828 genotypes in a red raspberry (Rubus idaeus) factorial mating design based on 42 full-sib families derived from seven female and six male parents harvested in one season in New Zealand. Narrow sense heritability estimates varied from moderately low [0.23 for percent budburst (PCBB)] to high [0.82 for mean berry weight (BWT)]. Highest genotypic correlations with total yield (TYLD) were found for mean cane length (0.60) followed by moderate correlations for PCBB (0.38), BWT (0.34) and fruit number per unit lateral (0.31). For these four components, the correlation between the product of the empirical breeding values (eBV) and TYLD was as good (0.67) as the correlation between the product of the seven yield components measured (0.68). Moderately high negative genotypic correlations were found between TYLD and TPH (–0.67), FRAP (–0.68), and TACY (–0.64), suggesting that breeding for high-yielding genotypes may result in reduced phytochemical levels. A pigment-deficient R. parvifolius × R. idaeus hybrid derivative parent (R. parv deriv) had the most influence on berry weight as a yield component. Removal of the R. parv deriv progeny from the analysis increased the contribution of berry weight to total yield. Heritability estimates were generally lower when the R. parv deriv crosses were omitted, particularly for number of canes BWT, TYLD, and the phytochemicals. Implications of R. parv deriv crosses on these results are discussed. Of the 828 genotypes, only five had an eBV for total yield greater than that of the best yielding parent, whereas 49 had larger berries than the best parent. None of the 828 genotypes had an eBV for yield components or phytochemicals less than that of the lowest parent, whereas 13 had a higher eBV associated with phytochemicals than that of the highest parent.
Ann Marie Connor, M. Joseph Stephens, Harvey K. Hall, and Peter A. Alspach
Variance components and narrow-sense heritabilities were estimated for antioxidant activity (AA), total phenolic content (TPH), and fruit weight in red raspberry (Rubus idaeus L.) fruit from offspring of a factorial mating design. Forty-two full-sib families utilizing seven female and six male parents were evaluated in each of two years in Motueka, New Zealand. In a single year, values within individual half-sib families ranged as widely as 25.3-79.4 μg·g-1 fruit for AA, 205-597 mg/100 g fruit for TPH, and 1.06-7.69 g for fruit weight. Analyses of variance for these three variates demonstrated significant parental source variation in both individual and combined year analyses. For AA and TPH, female parental effects accounted for ≈7% to 19% of total variation, while male effects accounted for ≈6% to 8%. A partially pigment deficient R. parvifolius L. derivative female parent accounted for some of these differences. Female × male parent interaction was not significant for AA and TPH and was marginally significant for fruit weight in combined year analysis. Year had a significant effect on the overall mean AA and TPH, but contributed less than genetic effects to the overall variation in all three traits. Interactions of year with genetic effects were not statistically significant for AA or TPH, indicating that between-year rank or scale changes among families were negligible. The largest proportion of variation was found within rather than among full-sib families. However, variation among plots within full-sib families accounted for 12% to 19% of total variation, indicating environmental differences accounted for some of the observed within-family variation in AA and TPH. Antioxidant activity and TPH were highly phenotypically correlated (r = 0.93); their genetic correlation (r = 0.59) implies that substantial additive genetic factors underlie the phenotypic correlation, but that nonadditive genetic or environmental influences are also important. Both AA and TPH were weakly negatively phenotypically correlated with fruit weight (r = -0.34 and -0.33, respectively), but the corresponding genetic correlations were close to zero. Thus, selection for both high AA or TPH and high fruit weight is possible. Narrow-sense heritability estimates based on variance components from combined year data were h 2 = 0.54, 0.48, and 0.77 for AA, TPH, and fruit weight, respectively. These estimates imply a rapid response to selection is possible.
Ann Marie Connor, Tony K. McGhie, M. Joseph Stephens, Harvey K. Hall, and Peter A. Alspach
We determined variance components and narrow-sense heritability estimates for total and individual anthocyanin (ACY) content and antioxidant activity (AA) in fruit from 411 genotypes in a red raspberry (Rubus idaeus L.) factorial mating design based on 42 full-sib families derived from seven female and six male parents, harvested in 2002 and 2003. Within half-sib family total ACY content ranged from ≈1-60+ mg/100 g fruit in both seasons. The four major ACYs quantified by high-performance liquid chromatography also showed wide ranges each year. Female and male parent contributions to variation in total and individual ACYs were significant (P ≤ 0.001) in combined year analysis, and together accounted for 29% to 48% of the total variation. A substantial proportion of the female contribution was attributed to the use of a pigment-deficient R. parvifolius L. × R. idaeus hybrid derivative as a female parent. Female × male interaction was nonsignificant and contributed negligibly to total variance. Year effects accounted for <2.5% of variation in ACYs and were only marginally significant. Year interactions were negligible. Within family variation (among plots and within plot) accounted for ≈50% of the variation in total ACY and 62% to 69% of the variation in individual ACYs. Combined year narrow-sense heritability estimates were high (h 2 = 0.54-0.90 for individual ACYs, 1.00 for total ACY) among all factorial genotypes, but moderate when the progeny of the R. parvifolius derivative were excluded (h 2 = 0.45-0.78 for individual ACYs, 0.74 for total ACY). The latter estimates are applicable to breeding programs in which pigment-deficient genotypes are rarely or never used in breeding. Parental main effects were significant for AA, together accounting for 19% of total variance; female × male interaction was nonsignificant. Year effects were marginally significant and year interactions nonsignificant; together these sources of variation contributed <2% of total variation in AA. The majority of AA variation was found within- and among-plots within family. The phenotypic correlation between AA and total ACY was r = 0.53, and ranged from r = 0.21-0.46 between AA and individual ACYs; genetic correlations between AA and the ACYs were similar to the phenotypic correlations, suggesting predominantly additive genetic effects accounted for the phenotypic correlations. Linear modelling for AA based on individual ACYs and their interactions explained ≈0.53 of AA variation, substantially less than that explained by total phenolic content (R 2 = 0.88). Our results show substantial variation and moderate to high narrow-sense heritability estimates for red raspberry ACYs, but ACY content and profile information are ineffective proxies and predictors for AA in red raspberry fruit.
Ann Marie Connor, Chad E. Finn, Tony K. McGhie, and Peter A. Alspach
Dietary anthocyanins (ACYs) may give health benefits through their antioxidant activity (AA) or other physiological effects. We examined AA and ACY profiles and contents in 16 blackberry and hybridberry (Rubus L. species) cultivars harvested in 2002 and 2003 in New Zealand and Oregon. Total ACY content varied widely among cultivars harvested from a single site in a single year (e.g., from 58 to 343 mg/100 g fruit Oregon in 2003). For the 12 cultivars common to both sites and years, cultivar and year within location significantly affected total ACY content, accounting for 40% and 10% of total variation, respectively. Cultivar interactions with both location and year within location were also significant, together accounting for 39% of variation. Cyanidin 3-O-glucoside and cyanidin 3-O-rutinoside were identified in all cultivars in both locations in at least 1 year. Compared with total ACY, cultivar accounted for more variation in these two ACYs (63% and 92%, respectively), while cultivar interactions together accounted for a smaller, but statistically significant, proportion of variation (23% and 7%, respectively). Cyanidin 3-O-sophoroside and cyanidin 3-O-(2G-glucosylrutinoside) were identified in only four cultivars. Cultivar effects accounted for 64% and 76% of variation in these ACYs, respectively, while cultivar interactions together contributed 18% and 24%, respectively. For AA, cultivar effects were not significant, contributing 11% of variation; in contrast, year effect and cultivar × environment interactions were significant, contributing 22% and 55% of total variation, respectively. Based on cultivar means for all 16 genotypes, the phenotypic correlation between AA and total ACY was positive but lower than that between AA and total phenolic content (TPH) (r = 0.63 and 0.97, respectively). Combinations of individual ACYs did not provide higher correlations with AA. Thus, ACY profiles and content are not as useful as TPH as a proxy measurement for AA.
James J. Luby, Peter A. Alspach, Vincent G.M. Bus, and Nnadozie C. Oraguzie
Incidence and severity of fire blight [Erwinia amylovora (Burr.) Winslow, Broadhurst, Buchanan, Krumwiede, Rogers, and Smith] following field infection were recorded using families resulting primarily from open-pollination of Malus sylvestris (L.) Mill. var.domestica (Borkh.) Mansf. cultivars and a few other Malus Mill. sp. The families were structured as three sublines, planted in three successive years (1992 to 1994), of a diverse population of apple germplasm established at HortResearch, Hawkes Bay, New Zealand. The incidence of fire blight varied among the sublines with the oldest planting exhibiting more fire blight. Flowering trees were more likely to be infected than nonflowering trees, in terms of both incidence and severity. Furthermore, the level of fire blight was related to flowering date, with later flowering trees having higher levels. Thus, family means and narrow-sense heritability estimates were computed after first adjusting the fire blight score for flowering date by fitting a linear model. Provenance of origin of the maternal parent explained little variation except that M. sieversii Lebed. families were more resistant than M. sylvestris var. domestica families in one subline. Family means computed using all trees, and those from only flowering trees were highly correlated. Families from open-pollination of M. honanensis Rehder and M. xhartwiggii Koehne females were among the more susceptible. Those from several European M. sylvestris var. domestica cultivars as well as from M. baccata (L.) Borkh. and M. toringoides (Rehder) Hughes females were among the more resistant families. Narrow-sense heritability estimates ranged from 0.05 to 0.85 depending on the subline, with most estimates between 0.12 and 0.36. They were higher in the two older sublines that consisted primarily of open-pollinated families from M. sylvestris var. domestica, and lower in the younger subline that consisted primarily of M. sieversii, due to lower incidence and severity in the latter subline. Breeders who consider potential complications of juvenility, tree size, and flowering date in relation to infection periods should be able to exploit field epidemics to perform effective selection.