Ex Parte Lambeth et al

Board of Patent Appeals and Interferences

Jun 6, 2006

09618307 (B.P.A.I. Jun. 6, 2006)

The opinion in support of the decision being entered today was not written
for publication and is not binding precedent of the Board.

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
__________

Ex parte CLEMENTS C. LAMBETH and
NICHOLAS C. WHEELER
__________

Appeal No. 2006-0138
Application No. 09/618,307
__________

ON BRIEF
__________

Before SCHEINER, MILLS, and GRIMES, Administrative Patent Judges.

GRIMES, Administrative Patent Judge.

DECISION ON APPEAL

This appeal involves claims to a tree breeding method, which the examiner has
rejected as lacking adequate description, nonenabled, and obvious. We have
jurisdiction under 35 U.S.C. § 134. We reverse the rejections for lack of adequate
description and nonenablement, but affirm the rejection for obviousness.
Background
“For decades, tree breeders have faced the dilemma of how to mate a select
group of individuals (parents) for the next generation of genetic improvement.”
Specification, page 1. “[T]he type of plant breeding strategy selected for use in a plant
breeding program depends upon a number of different factors. However, a common
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goal of a plant breeding program is to generally use a breeding method that will result in
the largest possible genetic gain using the smallest number of breeding crosses and the
least amount of time and money.” Page 7.
“Mating designs that have been commonly compared in the literature are open
pollination versus controlled pollination and, for the latter, full-sib crossing versus
polymix (a mixture of pollen from several males) crossing.” Id. “Polymix crossing is
done by mixing pollen from several males and applying the pollen to isolated females.
One of the advantages to polymix crossing is the simplicity of crossing and subsequent
testing of relatively few crosses.” Page 5.
“PMX [polymix] crossing provides excellent estimation of breeding value and
general combining ability (GCA) but not usually specific combining ability (SCA). . . .
Genetic gain potential for forward selection is good but not as high as that offered by the
commonly used full-sib systems.” Page 6. “The primary reason that PMX systems
result in less genetic gain from advanced generation selections versus full-sib systems
is due to the fact that the paternal parent’s GCA is unknown.” Id.
The specification discloses “a plant breeding design which utilizes PMX crosses
in conjunction with molecular marker technology to determine pedigree. Given a
sufficient number of reliable, polymorphic molecular markers, and modest care in
creation of pollen polymixes, paternity of all PMX progeny can be unambiguously
determined through molecular analysis. Therefore, the [disclosed method] provides a
plant breeding method that allows for pedigree control and estimation of breeding
values of the parental plants and their progeny.” Page 8.

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Discussion
1. Claim construction
Claims 20-31 are pending and on appeal. The claims stand or fall together
because Appellants have not argued them separately. See 37 CFR § 41.37(c)(1)(vii).
We will focus on claim 20, the only independent claim, which reads as follows:
20. A tree breeding method comprising:

(a) mixing pollen obtained from a breeding group comprising a plurality of
parental trees to obtain a pollen polymix;

(b) pollinating female reproductive structures from each parental tree in the
plurality of parental trees with the pollen polymix to obtain a plurality of progeny lots,
wherein each progeny lot comprises seeds obtained from a different cross between the
pollen polymix and each different parental tree of the plurality of parental trees;

(c) evaluating progeny trees grown from each of the progeny lots using
objective criteria to obtain a phenotype score;

(d) determining the pedigree of a plurality of progeny trees using DNA
analysis; and

(e) using the pedigree and phenotype score to identify elite trees for use in a
next generation of tree breeding.

Thus, claim 20 is directed to a method comprising (1) mixing pollen from a group
of male parental trees, (2) pollinating female parental trees with the pollen polymix,
(3) evaluating the resulting progeny trees “using objective criteria to obtain a phenotype
score,” (4) “determining the pedigree of a plurality of progeny trees using DNA analysis,”
and (5) using the combined phenotype score and pedigree information to choose which
progeny trees to use in the next round of breeding.

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2. Written description
The examiner rejected claims 20-31 under 35 U.S.C. § 112, first paragraph, on
the basis that the specification did not adequately describe the claimed method. The
examiner reasoned that the claims “are broadly drawn to a method of using a multitude
of non-exemplified DNA markers from a multitude of taxonomically unrelated and
physiologically and genetically divergent tree species.” Examiner’s Answer, page 4.
The examiner found that the specification did not provide a description of
corresponding breadth: “[T]he specification only provides guidance for SSRs [simple
sequence repeats; specification, page 9] from a single coniferous species, Pinus taeda.
No guidance is provided for the isolation or characterization of any other type of DNA
marker from any tree species.” Id., page 6. The examiner concluded that “[g]iven the
claim breadth and lack of guidance as discussed above, the specification fails to provide
an adequate written description of the genus as broadly claimed. Given the lack of
written description of the claimed products, any method of using them would also be
inadequately described.” Id., page 7.
Appellants summarize their position as follows: “Claims 20-31 are supported by
an adequate written description because (a) the art of tree breeding, including the use
of polymix crosses, was mature at the time the application was filed; (b) the art of DNA
analysis to distinguish individual trees was mature at the time the application was filed;
(c) no knowledge of DNA sequence is necessary to practice the methods of the
invention; and (d) the methods of the invention do not require a correlation between a
desirable trait of a plant and a DNA sequence.” Appeal Brief, page 9.

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“[The written description] inquiry is a factual one and must be assessed on a
case-by-case basis.” Purdue Pharma L.P. v. Faulding, Inc., 230 F.3d 1320, 1323, 56
USPQ2d 1481, 1483 (Fed. Cir. 2000). The specification need not describe the
invention in the same terms used in the claims, but the disclosure must convey with
reasonable clarity to those skilled in the art that the inventor was in possession of the
invention. See id.
The degree of specificity required to adequately describe an invention “varies
with the nature and scope of the invention at issue, and with the scientific and
technologic knowledge already in existence.” Capon v. Eshhar, 418 F.3d 1349, 1357,
76 USPQ2d 1078, 1084 (Fed. Cir. 2005). See also id. at 1359, 76 USPQ2d at 1085:
“[W]hat is needed to support generic claims to biological subject matter depends on a
variety of factors, such as the existing knowledge in the particular field, the extent and
content of the prior art, the maturity of the science or technology, the predictability of the
aspect at issue, and other considerations appropriate to the subject matter.”
In this case, we agree with Appellants that the examiner has not adequately
explained why a skilled worker in the field of tree breeding would have found the
present specification inadequate to show possession of the claimed method. The
evidence of record supports Appellants’ position that persons working in the field of tree
breeding knew how to use DNA markers to determine the pedigree of different trees.
See, e.g., Stoehr,1 page 188: “DNA markers represent powerful and useful genetic
markers for seed orchard management research. Especially useful for this purpose are

1 Stoehr et al., “Application of a chloroplast DNA marker in seed orchard management evaluations of
Douglas-fir,” Can. J. For. Res., Vol. 28, pp. 187-195 (1998)

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markers that are associated with the chloroplast, which is paternally inherited in
Douglas-fir . . . , providing a direct determination of male parentage.” In addition, the
specification cites numerous prior art references that are said to describe the use of
DNA markers in tree breeding. See pages 15-16 and 18-20.
Since the evidence of record shows that those skilled in the art were familiar with
the use of DNA markers to determine paternity in tree breeding research, we agree with
Appellants that those skilled in the art would not have considered a description of
specific DNA markers to be necessary in order to show possession of the claimed
method. The rejection for lack of adequate written description is reversed.
3. Enablement
The examiner also rejected claims 20-31 under 35 U.S.C. § 112, first paragraph,
on the basis that practicing the claimed method would have required undue
experimentation. The examiner argued that “[p]olymix-mediated breeding of trees for
phenotypic change is unpredictable, given the lack of available knowledge regarding
flower biology or pollination control in many tree species.” Examiner’s Answer, page 11.
“Furthermore, the use of polymix breeding may be confounded by the unequal
reproductive success of many parents’ pollen. . . . The claimed method relies upon the
assumption of equal reproductive success for its determination of pedigree and its
selection of elite trees for future breeding programs.” Id., pages 12-13. The examiner
cited Wiselogel2 as evidence that the Pinus taeda exemplified in the specification is
“unique regarding equal reproductive success of various parents’ pollen.” Id., page 13.

2 Wiselogel et al., “Probability of equal mating in polymix pollinations of loblolly pine (Pinus taeda L.),”
Silvae Genetica, Vol. 37, pp. 184-187 (1988)

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Finally, the examiner argued that “molecular marker-mediated selection in tree
breeding . . . is unpredictable,” and concluded that undue experimentation would have
been required to practice the full scope of the claimed method. Id., page 14.
Appellants argue that the amount of experimentation involved in practicing the
claimed method is not undue (Appeal Brief, pages 19-33), that the claimed method does
not require an assumption of equal reproductive success (Reply Brief, pages 1-2), and
that the claimed method does not involve marker-assisted selection (Appeal Brief,
pages 16-18).
We agree with Appellants that the examiner has not adequately explained why
the claimed method would require undue experimentation. The examiner’s first point –
that plant breeding involving polymix crosses is unpredictable – relates to plant breeding
in general, or at any rate to plant breeding designs involving polymix crosses. Yet the
evidence of record shows that polymix mating designs are commonly used in the field of
tree breeding. See Bridgwater,3 page 72 (Mating designs involving polymix crosses, or
polycrosses, are “in general usage.”). It therefore appears that those of skill in the art of
tree breeding consider the degree of unpredictability involved in polymix crosses to be
within the expected amount of experimentation.
With regard to the other two specific points made by the examiner – that the
claimed method relies on an assumption of equal reproductive success and that
molecular marker-mediated selection in tree breeding is unpredictable – we agree with
Appellants that these factors have no relevance to the claimed method. Appellants

3 Bridgwater, “Mating Designs,” in Fins et al. (eds.), Handbook of Quantitative Forest Genetics, pp. 69-95
(1992)

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argue, and we agree, that the claimed method does not rely on an assumption of equal
reproductive success. No such assumption is needed because the method involves a
step of determining, via DNA analysis, the paternity of the selected elite progeny prior to
using them in the next round of breeding. Because the paternity of the selected
progeny are determined based on DNA analysis, there is no need to assume that each
of the male parental trees was equally likely to be the male parent of a given progeny
plant.
Nor does the claimed method rely on molecular marker-mediated selection. The
examiner cites Strauss4 as evidence that “molecular markers are of limited availability
and of high cost, are restricted to particular genetic backgrounds, and that many traits of
interest to tree breeders are highly environmentally influenced, which would interfere
with selection of phenotypes to which markers could be reliably assigned.” Examiner’s
Answer, page 14.
However, the methods discussed by Strauss are not required to practice the
method claimed in this case. Strauss relates to linkage of quantitative trait loci (QTL)
with genetic markers:
By QTL we refer to polymorphic loci containing alleles that differentially
affect the expression of a continuously distributed phenotypic trait such as
height. Such loci are rarely observed directly, but are instead inferred to
exist via the correlation of linked genetic markers with phenotypic trait
values. By genetic markers we refer to effectively neutral, nuclear
genome markers, usually RFLPs.

Page 1051, right-hand column.

4 Strauss et al., “Limitations of molecular-marker-aided selection in forest tree breeding,” Can. J. For.
Res., Vol. 22, pp. 1050-1061 (1992)

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That is, the molecular marker-aided selection discussed by Strauss is a method
of selecting plants having QTL associated with a desired trait by screening for a marker,
such as an RFLP, that is linked to the desirable QTL. In the claimed process, by
contrast, the phenotypes of the progeny trees can be analyzed by any “objective
criteria,” which “include[s] the measurement of any plant characteristic or phenotype
with any detection/measurement device that provides statistically meaningful data
regarding the characteristic or phenotype being measured.” Specification, page 10. We
agree with Appellants that the claimed method does not require molecular marker-
assisted selection. Therefore, the degree of unpredictability or amount of
experimentation required to practice molecular marker-assisted selection is not a factor
in the enablement analysis of the claimed method.
We conclude that the examiner has not adequately explained why practicing the
claimed method would have required undue experimentation. We therefore reverse the
rejection for nonenablement.
4. Obviousness
The examiner also rejected claims 20-31 under 35 U.S.C. § 103 as obvious in
view of Bridgwater, El-Kassaby,5 and Stoehr. He reasoned that Bridgwater teaches the
general method of tree breeding using a pollen polymix, but “does not teach the use of
molecular markers to determine pedigree.” Examiner’s Answer, pages 20-21. The
examiner relied on El-Kassaby for its teaching of using isozyme testing “to determine

5 El-Kassaby et al., “Frequency-dependent male reproductive success in a polycross of Douglas fir,”
Theor. Appl. Genet., Vol. 83, pp. 752-758 (1992)

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the pedigree of progeny from a polymix cross of Douglas fir trees,” and Stoehr’s “use of
DNA markers to identify pedigree in Douglas fir.” Id., page 21.
The examiner also pointed out that Stoehr teaches that DNA markers provide
advantages over isozymes when determining pedigree; in particular, using markers
found in chloroplast DNA “provid[es] a direct determination of male parentage,” because
chloroplasts are paternally inherited. The examiner concluded that it would have been
obvious in view of the combined references to modify the polymix breeding method
taught by Bridgwater by adding a step of analyzing the pedigree of progeny trees, as
taught by El-Kassaby, using DNA markers such as those taught by Stoehr. See the
Examiner’s Answer, page 22.
We agree with the examiner that the cited references would have made the
method of claim 20 obvious to those of skill in the art. Bridgwater teaches that polymix
mating (or polycross mating) is a “mating design[ ] in general usage that do[es] not
provide information on male pedigrees, rather only the female pedigree is known.”
Page 72. Bridgwater teaches that a polycross mating “[p]rovides for good estimates of
gca [general combining ability] effects” (page 74) and provides for good estimates of
gains that arise from additive genetic variation (id.). Bridgwater also teaches that using
a polymix is less expensive than controlled-cross mating: “[T]he number of crosses
required to accomplish the objectives of polycross matings is usually several times
smaller than the numbers required for controlled-cross mating designs” (page 76).
However, Bridgwater teaches that polycross matings have disadvantages
compared to controlled crosses. First, “no estimate of sca [specific combining ability]
effects are possible since the male parents are unknown.” Page 74. Second, polycross

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mating “[d]oes not provide for control of male pedigrees if a single polymix is used on all
parents.” Page 75. The lack of control over male pedigree can reduce the expected
gains because a few of the male parents can produce most of the progeny. See id.
Thus, Bridgwater teaches that polymix mating designs have many advantages – cost, in
particular – but suffer from the drawback that the plant breeder does not know the male
pedigree of the selected progeny.
El-Kassaby teaches a method of determining the male pedigree in progeny of
polymix crosses. El-Kassaby used male parental plants that expressed different sets of
alleles for four enzymes;6 i.e., the combination of the four alleles was different for each
of the male parents. See Table 1. El-Kassaby then carried out a polymix mating and
analyzed the enzyme alleles present in the progeny (page 753, right-hand column, first
two paragraphs). El-Kassaby used the enzyme alleles in the progeny to determine
which of the male parents was the parent of each progeny seed. See Table 2.
Stoehr teaches a method of paternity analysis based on chloroplast DNA
markers. Stoehr teaches that analysis of chloroplast DNA “provid[es] a direct
determination of male parentage,” because “the chloroplast . . . is paternally inherited in
Douglas-fir.” Page 188, left-hand column, second paragraph. Stoehr exemplifies the
analysis of pedigree based on chloroplast markers in a “supplemental mass pollination”
technique.7 Based on the DNA-based analysis of male pedigree, Stoehr concluded that
“[o]utside-orchard contamination was reduced roughly by half . . . in clones treated with
SMP compared with controls.” Paragraph bridging pages 191 and 192.

6 Different alleles of enzymes are also known as isozymes. See, e.g., El-Kassaby, Table 1.
7 “Supplemental mass pollination (SMP), or the broadcast of viable pollen to nonisolated receptive strobili,
is a common crop-management practice in conifer seed orchards.” El-Kassaby, page 758.

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We agree with the examiner that these teachings support a prima facie case of
obviousness. Bridgwater teaches that polymix crosses are useful but suffer limitations
because the male pedigree is unknown. El-Kassaby teaches a method for determining
the male pedigree of the progeny of a polymix cross. Stoehr teaches that determining
male pedigree via DNA analysis has advantages over the isozyme analysis used by
El-Kassaby.
Therefore, it would have been obvious to a person of ordinary skill in the art to
improve the polymix method taught by Bridgwater by adding a step of determining the
male pedigree of the progeny, as taught by El-Kassaby, in order to solve the known
limitations that arise from not knowing the male pedigree of polymix progeny. It would
also have been obvious to determine male pedigree using DNA analysis, because
Stoehr teaches the advantages of using chloroplast DNA markers to analyze male
pedigree. Finally, it would have been obvious to the skilled tree breeder to consider
both phenotype data and male pedigree data in choosing which progeny to use in the
next round of breeding, because doing so would overcome the disadvantages
discussed by Bridgwater.
Appellants argue that none of the references individually teach or suggests all of
the steps of claim 20. See the Appeal Brief, pages 36-37. Appellants also argue that
none of the references teach or suggest step (e) of claim 20: using phenotype and
pedigree analysis together to choose which trees to use in the next round of breeding.
Id., pages 37-38.
These arguments are not persuasive. “Non-obviousness cannot be established
by attacking references individually where the rejection is based upon the teachings of a

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combination of references.” In re Merck & Co., Inc., 800 F.2d 1091, 1097, 231 USPQ
375, 380 (Fed. Cir. 1986). The test for obviousness is what the combined teachings of
the references as a whole would have suggested to those of ordinary skill in the art.
In re Keller, 642 F.2d 413, 425, 208 USPQ 871, 881 (CCPA 1981). Considered as a
whole, the references would have suggested all of the steps of claim 20, including
step (e), for the reasons discussed above.
Appellants also argue that “Bridgwater teaches away from the use of polymix
breeding by stating that ‘[i]f there is strong variation for general combining ability among
males and inbreeding depression is present, selection in base populations produced
from polycross matings will reduced expected gains since most selections may be
progenies of the same few pollen parents.’” Appeal Brief, page 36.
This argument is also unpersuasive. Bridgwater teaches that polymix breeding is
commonly used and has several advantages but also has limitations, including the one
discussed in the quoted passage, that arise from not knowing the male pedigree of
progeny. However, a person of ordinary skill in the art, familiar with the references
relied on by the examiner, would have realized that determining the male pedigree of
the progeny of a polymix cross would remedy the known problems of polymix mating
designs. Therefore, we do not agree with Appellants’ argument that Bridgwater would
have led away from a polymix-based breeding method.
Summary
We reverse the rejections for lack of adequate written description and
nonenablement. However, we agree with the examiner that the prior art would have
suggested the method of claim 20 to a person of ordinary skill in the art. Claims 21-31

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fall with claim 20. We therefore affirm the rejection of claims 20-31 under 35 U.S.C.
§ 103.
No time period for taking any subsequent action in connection with this appeal
may be extended under 37 CFR § 1.136(a).
AFFIRMED

Toni R. Scheiner )
Administrative Patent Judge )
)
)
) BOARD OF PATENT
Demetra J. Mills )
Administrative Patent Judge ) APPEALS AND
)
) INTERFERENCES
)
Eric Grimes )
Administrative Patent Judge )

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