General Summary and Conclusions

The inheritance of plant architecture and fruit yield (yield components)
in melon (*Cucumis melo* L.; 2n = 2x =24) was examined by generation
means analyses, variance component analyses, and QTL mapping using cross
progeny derived from line USDA 846-1 (P~1~), possessing a unique fractal
architectural habit, and a standard vining Western Shipping melon type,
"Top Mark" (P~2~). The, incorporation of genes resident in fractal melon
types may provide an avenue for increasing yield potential in commercial
melon.

Generation mean analyses were performed using two-location (Arlington
and Hancock Wisconsin) performance results of P~1~ and P~2~ and their
cross-progeny (BC~1~P~1~, BC~1~P~2~, and F~2~). Significant (p ≤ 0.01 or
p ≤ 0.05) location and location x generation interactions necessitated
that analyses were performed by location for all traits examined (days
to anthesis, fruit number and weight per plant, and average weight per
fruit), except for primary branch number which was analyzed both by
location and using combined location values. In general, progeny
distributions (BC~1~P~1~, BC~1~P~2~, and F~2~) of all traits were
normally distributed without the presence of distinct bimodal peaks.
Individual BC~1~P~1~, BC~1~P~2~, and F~2~ progeny were observed that
reached or transgressed the phenotypic extremes of either parent for
most traits and locations.

Genetic models developed to define the inheritance of the different
yield components varied across environments. However, in general, a
simplistic additive-dominance model did not adequately explain the
observed variation for any of the traits examined. Genetic models that
included some type of epistatic parameter (i.e., additive x additive,
additive x dominance, or dominance x dominance) were useful in
describing the observed variation for all traits. Nevertheless, while
dominance and epistatic effects mainly controlled days to anthesis,
fruit weight per plant, and average weight per fruit, additive gene
effects were most important for governing primary branch number, and
fruit number per plant. The presence of epistatic effects detected for
days to anthesis, fruit weight per plant, and average fruit weight will
likely make selection for these traits difficult in this population.

Variance component analyses were applied to F~3~ family yield component
data collected at Arlington (AR) and Hancock (HCK), Wisconsin. The
distributions of F~3~ family means for all traits were normally
distributed indicating the quantitative genetic nature of the yield
components examined. Analyses of variance were performed by locations
for all traits examined due to significant (p ≤ 0.01 or p ≤ 0.05)
location effects and location x generation interactions. Although
environment by F~3~ family interactions (G x E) were observed for
primary branch number, fruit number, and average weight per fruit,
Spearman (rank) correlations between environments indicated that the
interactions between family and environment were mostly due to changes
in magnitude and not in direction of the response in different
environments. In contrast, Spearman (rank) correlations coefficients
between locations, fruit weight per plant, percentage of plants with
predominantly crown fruit set, and percentage of plants with early
maturing fruit were mainly affected by G x E interactions due to changes
in the direction of the response.

Variance component analyses indicated that primary branch number and
fruit number per plant exhibited mainly additive genetic variance, while
fruit weight per plant and average fruit weight demonstrated mainly
dominance genetic variance. Broad-sense heritabilities were 0.63 (AR)
for days to anthesis, 0.64 (AR) for percentage of plants with early
pistillate flowering, 0.60 (AR) and 0.66 (HCK) for percentage of plants
with predominantly crown fruit set, 0.83 (AR) and 0.85 (HCK) for average
weight per fruit, and 0.62 (AR) and 0.72 (HCK) for percentage of plants
with early maturing fruit. Narrow-sense heritabilities were 0.91 (AR)
and 0.86 (HCK) for primary branch number, 0.72 (AR) and 0.51 (HCK) for
fruit number per plant, 0.45 (AR) and 0.28 (HCK) for fruit weight per
plant, and zero (AR) and 0.06 (HCK) for average fruit weight. Broad- and
narrow-sense heritability estimates indicate that it may be possible to
identify and select highly branched-fractal genotypes with early,
uniform flowering, and concentrated fruit-setting ability in this
population. However, the lower heritabilities and G x E interactions
detected for earliness, fruiting, and maturity traits suggests that the
efficient development of fractal melon genotypes with improved
characteristics may be accomplished by the incorporation (fixation of
alleles) of high number of primary branch number while maintaining
population variability for all other horticulturally preferred
characteristics. A recurrent selection scheme incorporating a selection
index might allow for the increase of desirable alleles in this
population. Subsequently, family or pedigree selection may be performed
for line extraction using multiple evaluation environments with
extensive replication to minimize environmental effects.

A set of 81 recombinant inbred lines (RIL) developed for this study was
used to construct a 181-point genetic map consisting of 114 RAPD, 35
SSR, and 32 AFLP markers (Chapter III). Fifteen linkage groups spanned
1,032 cM with a mean marker interval of 5.7 cM. A saturated genetic map
of melon is predicted to be 1,500 to 2,000 cM in length consisting of 12
linkage groups. Thus, this map must be considered unsaturated. Better
genomic coverage could be accomplished by increasing the size of the RIL
and map saturation with codominant markers. This is currently being
accomplished by a project designed to add AFLP and SSR to the map
described herein.

The RIL population was grown in Hancock, Wisconsin and El Centro,
California to examine sex expression and other yield components. Sex
expression was influenced by four genomic regions, one (*exs8.3*)
corresponding to the *a* locus in linkage Group 8. This result supports
the hypothesis that pistillate/hermaphroditic flowering is controlled at
the *a* locus and provides evidence for the role of other genomic
regions (i.e., modifying genes) in determining this sex expression type
in melon. It is possible that in this RIL population the genomic regions
identified in LG4 (*exs4.1*), LG6 (*exs6.2*), and LG9 (*exs9.4*) operate
to modify the action of the *a* locus depending on environmental
conditions (e.g., temperature, humidity, and photoperiod).

Estimates of effective factors (n) provided by biometrical methods (e.g.
generation mean analysis and variance component analysis) are usually
biased downward due to dominance, epistasis, G x E interactions, and
linkage (Chapters I and II). While biometrical estimates of (n)
controlling primary branch number ranged between two to four, fruit
number and weight per plant and average weight per fruit estimates of
(n) were negative or zero. However, since the phenotypic distributions
of F~2~ (Chapter I) progeny, F~3~ families (Chapter II) and RIL (Chapter
III) derived from a P~1~ x P~2~ mating for all yield-related traits
examined were normally distributed, it was concluded that such traits
have a complex inheritance that is controlled by more than two genes.

A total of 34 QTL were detected in both locations for yield components
(primary branch number = 7, fruit number per plant = 10, fruit weight
per plant = 9, average weight per fruit = 5, and percentage of mature
fruit per plot = 3) (Chapter III). The detection of 97 pairs of putative
QTL possessing joint-QTL epistatic effects and 38 pairs of putative QTL
possessing interaction-QTL epistatic effects confirmed the empirical
findings obtained from a generation means analyses regarding the
presence of significant epistatic effects for most of the traits
examined (Chapter I). Moreover, fruit weight per plant, average weight
per fruit, and percentage of mature fruit per plot possessed 84% of all
the putative epistatic QTL identified, which also recapitulates the
results of generation means analyses (Chapter I), and indicates that
additional QTL with smaller effects may be operating to control these
traits in this population. Thus, QTL analysis allowed for the dissection
of individual loci and a rather precise description of the numbers,
magnitudes, and distributions QTLs affecting yield components in melon.
This information, along with genetic estimates for yield related traits
(Chapters I and II) will be used to develop backcross derived lines with
allelic arrays for horticulturally desirable characteristics.

The significant positive phenotypic correlations observed among primary
branch number, fruit number per plant, and fruit weight per plant, and
negative phenotypic correlations between primary branch number and
average weight per fruit and between fruit number and average weight per
fruit (Chapters I, II, and III) were consistent with the genomic
locations and effects (negative vs. positive) of the QTLs detected
(Chapter III). Given these results, it is likely that genes resident in
fractal melon types could be used for increasing yield in U.S. Western
Shipping type germplasm. For instance, the molecular markers associated
with QTLs for primary branch number (*pb1.1*, *pb1.2*, *pb2.3*, and
*pb10.5*) are candidates for assisting conventional breeding efforts
that seek to modify plant architecture in melon. Likewise, consistent
QTL for sex expression (*exs4.1* and *exs8.3*), fruit number per plant
(*fn1.1*, *fn1.3*, and *fn5.6*), fruit weight per plant (*fw1.1*,
*fw5.6*, *fw6.7*, and *fw8.8*), and average weight per plant (*awf1.2*
and *awf4.3*) identified herein will likely value for marker-assisted
selection in advanced populations derived from USDA 846-1 and/or "Top
Mark". However, additional validation of these putative QTL associations
is needed before they can be strategically deployed in a breeding
program to improve yield in melon.

Commercial breeding strategies are typically dedicated to the
incorporation of horticulturally important traits controlled by single
genes (e.g., disease resistance) by backcrossing pedigree selection for
use in hybrid production. The markers associated with yield components
reported herein could be used in MAS to improve yield. However, this
would require considerable investment of resources and labor from the
private and public sectors. Such an investment would have a high
probability of success only when extreme fractal phenotypes and markers
associated with yield component QTL are used for both population
improvement and inbred line development. The retention of
characteristics (e.g., fruit quality) that typify commercial U.S.
Western Shipping type melon varieties along with the introgression of
architectural and fruiting characteristics from fractal type melons will
be essential for commercial success. The ideal fractal melon variety
will be monoecious, early flowering, highly branched, and produce early,
concentrated yield. Such genotypes would be excellent for once-over
and/or machine harvesting operations since they would ideally set three
fruit to four fruit "simultaneously" (within a 1-2 day period of time)
near the crown of the plant (i.e., concentrated setting). However,
development of such germplasm would require a long-term commitment,
perhaps 5-10 years.