Ex Parte Chaky et al

Patent Trial and Appeal Board

Nov 25, 2016

13339548 (P.T.A.B. Nov. 25, 2016)

United States Patent and Trademark Office
UNITED STATES DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
Address: COMMISSIONER FOR PATENTS
P.O.Box 1450
Alexandria, Virginia 22313-1450
www.uspto.gov
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
13/339,548 12/29/2011 Julian M. Chaky PHI 2913 US NA
(35290-056
2872
26691 7590 11/25/2016
POTTER ANDERSON & CORROON LLP
ATTN: JANET E. REED, PH.D.
P.O. BOX 951
WILMINGTON, DE 19899-0951
EXAMINER
ROBINSON, KEITH O NEAL
ART UNIT PAPER NUMBER
1661
MAIL DATE DELIVERY MODE
11/25/2016 PAPER
Please find below and/or attached an Office communication concerning this application or proceeding.
The time period for reply, if any, is set in the attached communication.
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte JULIAN M. CHAKY, MOLLY RYAN-MAHMUTAGIC,
EDWIN JOSUE MENDEZ, SALLY ANNE SANTIAGO-PARTON,
JOSHUA M. SHENDELMAN, JOHN B. WOODWARD,
and YANWEN XIONG
Appeal 2015-001609
Application 13/339,548
Technology Center 1600
Before ERIC B. GRIMES, RICHARD M. LEBOVITZ, and
KRISTI L. R. SAWERT, Administrative Patent Judges.
LEBOVITZ, Administrative Patent Judge.
DECISION ON APPEAL
This appeal involves claims directed to a method for identifying
improved resistance to one or more aphid biotypes comprising a step of
detecting a marker or SNP in a soybean plant or germplasm. The Examiner
finally rejected the claims as obvious under 35 U.S.C. § 103(a). We have
jurisdiction under 35 U.S.C. § 134. The obviousness rejection is affirmed.
STATEMENT OF CASE
Appellants appeal from the Examiner’s rejection of claims 1—3
and 8—22 under 35 U.S.C. § 103(a) (pre-AIA) as obvious in view of
Appeal 2015-001609
Application 13/339,548
Hill et al. (U.S. Publ. Pat. App. No. 2006/0015964 Al, publ. Jan 19,
2006) (“Hill ’964”) and Hill et al. (A New Soybean Aphid (Hemiptera:
Aphididae) Biotype Identified, 103 J. Econ. Entomol. 509—515 (2010))
(“Hill (2010)”). Final. Rej. 4.
Claim 1, the only independent claim on appeal, reads as
follows:
1. A method of identifying a first soybean plant or
germplasm that displays improved resistance to one or more
soybean aphid biotypes, the improved resistance comprising
one or more of improved antibiosis resistance and improved
antixenosis resistance, the method comprising detecting in the
first soybean plant or germplasm, or a part thereof, at least one
Rag haplotype that is associated with the improved soybean
aphid resistance, the at least one Rag haplotype comprising
marker loci selected from the group consisting of:
(a) one or more marker loci selected from the group
consisting of S14181-1-Q1, S13871-1-Q1, S14161-1-Q10,
S09515-1-Q1, S14151-1-Q1, S14151-2-Q4, S07164-1-Q12,
S14182-1-Q1, S00812-1-A, and S02780-1-A;
(b) one or more marker loci selected from the group
consisting of SOI 190-1-A, S14761-001-Q001, S14771-001-
Q001, S07165-1-Q3, S14778-001-Q001, and SOI 164-1-Q1;
(c) one or more marker loci selected from the group
consisting of S13662-1-Q3/Q6, S13663-1-Q1, S11411-1-Q1,
S13664-1-Q1/Q002, S13672-1-Q1/Q2/Q3, S13674-1-Q1/Q007,
and S13675-2-Q1;
(d) one or more SNP loci located at physical positions
5516385, 5516818, 5598980, 5602544, 5605203,5605275,
5608106, 5630404, 6754454, and 6671535 on LG-M of the
soybean genome;
(e) one or more SNP loci located at physical positions
28187733, 28829625, 28837383, 29097652, 29678319, and
29825175 on LG-F of the soybean genome; and
(f) one or more SNP loci located at physical positions
5140274, 5919650, 5960726, 6066531, 6231641, 6524877, and
6542422 on LG-J of the soybean genome.
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Application 13/339,548
REJECTION
Claim 1, the only independent claim on appeal, is directed to a method
of identifying a first soybean plant or germplasm that displays improved
resistance to one or more soybean aphid biotypes. The method involves
detecting a “Rag haplotype” comprising detecting marker loci selected from
a list of marker loci and SNPs (single nucleotide polymorphisms).
“Rag” is the notation for three different soybean aphid resistance
genes that had been mapped to the soybean genome prior to the filing date of
the application. Spec. 3:17—19. The three known aphid resistance genes are
Ragl, Rag2, and Rag3. Id. at 3:20-29. The Specification explains that
soybean resistance to aphids is important because soybean is a major cash
crop and aphids are a widely distributed soybean pest that can cause severe
damage and loss of soybean crops. Id. at 1:16 to 2:28. Hill ’964 teaches that
aphid Rag resistance genes can be introduced by selective breeding into
soybean plants to create inbred soybean plant lines that are resistant to
aphids. Hill ’964 117.
The Examiner rejected the claims as obvious in view of Hill ’964 and
Hill (2010). The Examiner found that Hill ’964 identified Rag markers
associated with resistance to soybean aphids. Final Rej. 7. The Examiner
acknowledged that Hill ’964 does not describe the Rag markers recited in
the claims, but found that the skilled worker would have been motivated to
find other Rag markers in view of Hill ’964’s teaching (id.) that “[ojther
markers of linkage group M may also be used to identify the presence or
absence of the gene.” Hill ’964 112. The Examiner relied on Hill (2010) in
rejecting claim 3 which specifies that the improved soybean aphid resistance
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comprises improved resistance to at least two of soybean aphid biotypes 1,
2, 3, and X.
Appellants contend “it would not have been reasonable to expect that
the skilled artisan would successfully arrive at the specific and novel
markers recited in Applicants’ claims. This is because the markers recited in
Applicants’ claims are novel markers that are not taught or even suggested
by Hill 2006 or Hill 2010.” Appeal Br. 10— 11. Appellants further argue that
“Genetic screening can be unpredictable. In many cases, genetic screening
efforts only fortuitously yield genetic loci that contribute to specific
phenotypes or functions.” Reply Br. 6.
DISCUSSION
The Specification describes genetic markers that can be used to
identify and select soybean plants with improved antibiosis and/or
antixenosis resistance to one or more biotypes of soybean aphid. Spec. 5:5—
13. “Antibiosis (non-choice) is the plant’s ability to reduce the survival,
reproduction, and fecundity of the insect. Antixenosis (choice) is the plant’s
ability to deter the insect from feeding or identifying the plant as a food
source.” Id. at 3:13—16. A “biotype” is defined in the Specification as a
“subspecies of soybean aphid that shares certain genetic traits or a specified
genotype.” Id. at 3:8—9. Aphids can characterized as a single biotype based
on their resistance to a plant’s antibiosis or antixenosis effects.
The genetic markers to select aphid resistant soybean strains are
recited in the rejected claims. While the Specification does not disclose how
these markers were specifically identified, it does not appear to have been
disputed that the markers are derived from the three different soybean aphid
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resistance genes (Ragl, Rag2, and Rag3) which had previously been mapped
to specific locations in the soybean genome. Id. at 3:17—29; 12:27 to 13:7;
30:20 to 32:12.
Hill ’964 describes a method of identifying markers associated with
soybean aphid resistance genes Ragl and Rag2. Hill ’964 H 11, 12;
Example 3 flflf 85—86); Example 4 flflf 87—90). The Examiner acknowledges
that the claimed markers identified by the inventors for the known aphid
resistance genes are novel, but found it would have been obvious to have
identified them utilizing Hill ’964’s method. Final Rej. 7.
We agree with the Examiner’s determination that the claims would
have been obvious to one of ordinary skill in the art at the time of the
invention based on the cited publications.
The claims in this appealare directed to novel nucleic acid sequences;
specifically, markers and SNPs that co-segregate with the known soybean
aphid resistance genes Ragl, Rag2, and Rag3. The starting materials used to
obtain these sequences appear to have been available. For example,
numerous soybean germplasms from which to obtain the marker sequences
were known at the time of the invention. See Hill ’964, 52 (Table 1); Hill
(2010), Table 1; see also Spec. 50:17—18 (disclosing the use of “Thirty five
hundred soybean plant introductions (Pis). . . obtained from the USD A
Soybean Germplasm Collection.”). . The soybean aphid resistance linkage
groups from which the markers were obtained were also known as
established by admissions in the Specification and by Hill ’964. Spec. 3:17—
29; 5:15 to 12:9 (indicating that the claimed markers and sequences are
present in soybean genomic regions known to contain the Rag genes). For
example, the Specification discloses that a variety of the claimed sequences
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reside in chromosomal linkage group LG-M. Id. at 5:17—18; 5:24—8:10.
Hill ’964 identified LG-M as the region in which Ragl and Rag2 reside.
Hill ’96411 11,20.
Hill ’964 provides evidence that techniques used to isolate markers
from the linkage groups comprising the known soybean resistance genes
were conventional and routine, as were the methods to use the markers to
identify aphid resistant plants. Hill ’964 H 11, 12; Example 3 (H 85—86);
Example 4 (H 87—90). Thus, the markers recited in the claims are a product
of using known materials and conventional technology which had
successfully been applied to obtain different markers for the same known
Rag genes within the same identified linkage groups.
Appellants’ argument that the sequences and positions of the markers
recited in the rejected claims were unknown and not suggested by the cited
Hill ’964 and Hill (2010) does not persuade us that the Examiner made
reversible error in determining that the claims are obvious. A novel
nucleotide sequence is not necessarily non-obvious to one of ordinary skill
in the art. In re Kubin, 561 F.3d 1351 (Fed. Cir. 2009). In this case, the
claimed markers were identified from linkage groups known to co-segregate
with the aphid resistance genes. As found by the Examiner, Hill ’964
expressly teaches that that “[ojther markers of linkage group M may also be
used to identity the presence or absence of the [aphid resistance] gene.” Hill
’964 112; Final Rej. 7. Appellants have not directed us to evidence in this
record that the methods and materials utilized to identify the recited markers
departed from the conventional materials and technology described in Hill
’964 and as available prior to the application filing date.
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Appellants contend that “a person of ordinary skill in the art would
not have a reasonable expectation of success to arrive at the invention as
claimed, given the often unpredictable nature of genetic screening.” Reply
Br. 6—7. However, Appellants have not provided evidence of
unpredictability. An argument made by counsel in a brief does not substitute
for evidence lacking in the record. Estee Lauder Inc. v. L ’Oreal, S.A., 129
F.3d 588, 595 (Fed. Cir. 1997). On the other hand, Hill ’964 describes using
the technique to identity markers. Consequently, a preponderance of the
evidence does not support Appellants’ argument that it would have been
unpredictable to have obtained the markers recited in the rejected claims.
Appellants argue that “[wjithout recognizing the usefulness of the
markers, as the markers were unknown, a person of ordinary skill in the art
would not have a reasonable expectation of success to arrive at Appellants’
invention as claimed.” Reply Br. 7. This argument does not persuade us
that the Examiner erred. Markers for the aphid resistance genes were known
to be useful to identify soybean plants’ resistance to aphids. See generally
Hill ’964. While the specific marker sequences recited in the claims were
unknown, they are derived from the known aphid resistance genes and
linkage groups, and it would have been obvious to have identified the
markers utilizing Hill ’964’s method for its expected success. It was not
unexpected, based on Hill ’964, that markers for soybean aphid resistance
genes could be routinely identified. We have not been directed to evidence
that would counter the teaching in Hill ’964 of the successful identification
of marker sequences utilizing its technology.
In the Reply Brief, Appellants assert that “[a]s the presently claimed
methods use markers outside of the paragraph [0012] region on LG-M, and
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Hill [’964] does not actually teach or suggest using such markers,
Appellants[’] use here should be nonobvious over the cited art.” Reply Br.
7. However, Appellants did not direct us to evidence that the markers are
outside the region of LG-M defined by Hill ’964. Nonetheless, even if they
did, the recited markers are present in the linkage groups disclosed by
Hill ’964 to contain the known Rag genes. Appellants did not establish that
it was surprising that useful markers would reside outside the specific
genomic regions described in Hill ’964.
Claim 2
Claim 2, depends from claim 1, and further recites “wherein the
improved soybean aphid resistance comprises both improved antibiosis
resistance and improved antixenosis resistance.”
The Examiner states that neither of the cited publications describe
improved antibiosis and antixenosis resistance. Final Rej. 9. However, the
Examiner found it would have been obvious “that having both improved
antibiosis resistance and improved antixenosis resistance would allow a
soybean plant to have greater resistance to soybean aphid ... as opposed to
only having one or the other.” Id. The Examiner further found that Hill
(2010) teaches both antibiosis and antixenosis screening of soybean for
aphid resistance, providing a reason to have identified plants with both.
Ans. 9.
Appellants contend that Hill (2010) “does not teach or suggest
experiments to measure antibiosis, which concerns an insect’s increased
mortality, shortened longevity or decreased reproduction capacity in
response to a resistant plant.” Reply Br. 9-10. Rather, Appellants argue that
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Hill (2010) “teaches two kinds of choice tests conducted by the authors,
indicating that antixenosis, which concerns an insect’s non-preference for a
resistant plant compared to a non-resistant plant, is the focus of their
experiments.” Id. at 9.
This argument does not convince us that the Examiner erred.
Hill (2010)’s experiments were designed to characterize a new
soybean aphid biotype. Hill (2010) 509, Abstract & 510, col. 2,11. 2—6.
Thus, even if Hill (2010)’s experiments only looked at antixenosis, the
reason is that the tests were performed to identify the aphid as a new
biotype.
Choice and nonchoice tests conducted in this study
characterized the colonization of a soybean aphid isolate,
collected from the overwintering host Frangula alnus P. Mill in
Springfield Fen, IN, on different aphid resistant soybean
genotypes. This isolate readily colonized plants with the Rag2
resistance gene, distinguishing it from the two biotypes
previously characterized and indicating that it represented a
new biotype named biotype 3.
Id., Abstract.
Nonetheless, we note that Hill (2010) report in Experiment 3 that the
results “indicated that LD05-16611 had antibiosis-type resistance.” Id. at
513. Thus, contrary to Appellants’ argument, Hill (2010) looked at both
antibiosis and antixenosis.
Hill (2010) stated that the identification of a new aphid biotype
indicated that “there is high variability in virulence in soybean aphid
populations present in North America, posing a significant challenge to
soybean breeders developing soybean aphid resistant cultivars.” Id. at 514,
col. 2 (first full paragraph). Because of this finding, Hill (2010) further
stated that the known Rag aphid resistance genes might not be sufficient to
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provide long-term resistance to aphids. Id. Consequently, Hill (2010)
suggested identifying new aphid resistance genes. Id. Hill (2010)
specifically discusses “[resistance gene stacking” as “a method used by
breeders to improve the durability of plant disease resistance,” in which a
plant is bred and selected to have more than one resistance gene, such as
Ragl, Rag2, etc. Id. Based on this disclosure, the skilled worker would
have had reason to have selected plants with more than one type of aphid
resistance in an effort to “stack” plants with more than one resistance gene —
as determined by the Examiner. Hill (2010) specifically mentions antibiosis:
Resistance in ‘Dowling’ had strong antibiosis that limited aphid
colonization on plants in nonchoice tests. Detailed analysis of
the effects of antibiosis on aphid biology indicated that the
resistance in Dowling significantly reduced aphid survival,
longevity, fecundity, and nymphal development.... The aphid
resistance in Dowling was shown to be controlled by a single
dominant gene named Ragl.
Id. at 510, col. 1,11.2-10.
Hill (2010) also characterizes plants with antibiosis and antixenosis
phenotypes:
However, colonization on soybean genotypes with Ragl was
significantly lower than on Williams 82 or on genotypes with
Rag2 in nonchoice tests (Fig. 1, Tables 4 and 5). These results
seemed to indicate that some soybean genotypes with Ragl
expressed antibiosis-type resistance with little, if any,
antixenosis-type resistance.
Id. at 514, col. 2,11. 3—9.
In sum, the preponderance of the evidence supports the Examiner’s
determination that claim 2 would have been obvious to one of ordinary skill
in the art.
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Claims 11—14
Claims 11—14 recite specific sequences as the haplotype markers
(SEQ ID NOS). Appellants contend that these sequences are not disclosed
or suggested by Hill ’964 and Hill (2010). Appeal Br. 13. While the
sequences had not been identified in the cited publication as Rag haplotypes
associated with improved aphid resistance, the sequences are an obvious
result of applying the conventional technique described in Hill ’964 to
known starting materials. Consequently, we conclude that the claims are
obvious for the same reasons discussed above for claim 1.
Claim 20
Claim 20 depends on claim 1, from claims 18 and 19, and further
recites that the first soybean plant of claim 1 is crossed with a “second
soybean plant or germplasm compris[ing] an exotic soybean strain or an elite
soybean strain.” The Examiner found that Hill ’964 teaches high yield
parents which “read” on elite strains and that such crosses are conventional.
Final Rej. 8; Ans. 11—12.
Appellants contend that “[a] person of ordinary skill in the art would
understand that some elite strains do not display high yield.” Appeal Br. 13.
This argument is not persuasive. As found by the Examiner (Ans.
11), Hill ’964 teaches:
The information disclosed herein regarding RAG loci is used to
aid in the selection of breeding plants, lines and populations
containing Aphis glycines resistance for use in introgression of
this trait into elite soybean germplasm, or germplasm of proven
genetic superiority suitable for variety release.
Hill ’964,1 13.
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Claims 21 and 22
Claims 21 and 22 depend ultimately from claim 1, and recite that the
first soybean plant or germplasm is selected from a specific list of soybean
varieties identified by PI (“plant introduction,” Spec. 50:17) numbers. The
claims require detecting “at least one Rag haplotype that is associated with
the improved soybean aphid resistance, the at least one Rag haplotype” in
one of the listed Pi’s.
The Examiner determined that “it would have been obvious to one of
ordinary skill in the art to select soybean Pis because it is known that Pis are
sources for disease and pest resistant genes.” Final Rej. 8. The Examiner
also found that Hill ’964 “provides evidence that there are many Pis that
possess resistance to soybean aphids as shown in Table 1.” Ans. 12.
Appellants contend that the skilled worker would not have been able
to predict that the specific Pis recited in the claims would have resistance to
one or more soybean aphid biotypes. Appeal Br. 13—14.
As found by the Examiner, Hill ’964 teaches a list of Pis that are
sources of resistance to soybean aphid. Hill ’964, || 50-53. Hill ’964
teaches that screening using its markers can be performed on any of the
parental lines disclosed by Hill ’964 or known in the art. Id. at || 74, 75.
Hill (2010) also teaches Pis that are resistant to the aphid. Hill (2010) 511
(Table 1), 512 (Table 2), 513 (Tables 3 and 4). The germplasms for the Pis
are available from the USDA Soybean Germplasm Collection, Urbana, IL.
Id. at 511 (footnote to Table 1). Consequently, as found by the Examiner, it
would have been obvious to one of ordinary skill in the art to have selected a
known PI for screening with markers. While the Examiner did not establish
that the specific PI lines were known to be resistant to aphids or to possess
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one of the specifically claimed markers, it would have been obvious to have
screened for one based on the success of Hill ’964 in doing so, and Hill
’964’s disclosure that screening can be performed on other parental lines.
Because the conventional technology of identifying aphid resistance
and screening for resistance markers — as taught in Hill (2010)
(characterizing aphid resistance in various soybean varieties) and Hill ’964 —
has been applied to known and available soybean lines, it would have been
reasonably expected that other varieties would be routinely selected using
these known methods. While the identification of these markers in the
recited Pis may be new, Appellants have not provided evidence that it was
unpredictable that they could be identified.
SUMMARY
Because Appellants did not identify a reversible error in the
Examiner’s rejection, we affirm the rejection of claims 1, 11—14, 20, 21, and
22 as obvious. Claims 2, 3, and 8—10, and 15—19 fall with claim 1 because
separate reasons for their patentability were not provided. 37 C.F.R.
§ 41.37(c)(l)(iv).
TIME PERIOD
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a)(l)(iv).
AFFIRMED
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