( 12 ) United States Patent
`Funk et al .
`
`US 10,982,187 B2
`( 10 ) Patent No .:
`( 45 ) Date of Patent :
`Apr. 20 , 2021
`
`US010982187B2
`
`( 54 ) BOS TAURUS VARIETY ' HO840003150607238
`AND METHODS OF USE THEREOF
`( 71 ) Applicant : ABS Global , inc . , DeForest , WI ( US )
`( 72 ) Inventors : Devan Charles Funk , DeForest , WI
`( US ) ; Katrina Dattilo , Waunakee , WI
`( US )
`( 73 ) Assignee : Genus PLC , Basingstoke ( GB )
`Subject to any disclaimer , the term of this
`( * ) Notice :
`patent is extended or adjusted under 35
`U.S.C. 154 ( b ) by 0 days .
`( 21 ) Appl . No .: 16 / 365,306
`( 22 ) Filed :
`Mar. 26 , 2019
`( 65 )
`Prior Publication Data
`US 2020/0305399 A1
`Oct. 1 , 2020
`
`( Sep. 2013 ) updated Dec. 1 , 2018 , downloaded ( see comment
`below ) at aipl ( dot ) arsusda ( dot ) gov / reference / recessive_haplotypes
`ARR - G3.html .
`Gay et al . , “ Development of a Lifetime Merit - based selection index
`for US dairy grazing systems , ” J. Dairy Sci . 97 : 4568-4578 ( 2014 ) .
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`( 2010 ) .
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`“ Genetic relationships between feral cattle from
`Chirikof Island , Alaska and other breeds , ” Animal Genetics 38 : 193
`197 ( 2007 ) .
`McClure et al . , " SNP Data Quality Control in a National Beef and
`Dairy Cattle System and Highly Accurate SNP Based Parentage
`Verification and Identification , ” Frontiers in Genetics 9 ( 84 ) : 1-14
`( 2018 )
`Niemann , “ Transgenic pigs expressing plant genes , ” Proc Natl Acad
`Sci US A 101 : 7211-7212 ( 2004 ) .
`Park , et al . , “ Role of stem cells in large animal genetic engineering
`in the TALENS - CRISPR era , ” Reprod Fertil Dev 26 : 65-73 ( 2014 ) .
`Park et al . , “ Genome sequencing of the extinct Eurasian wild
`aurochs , Bos primigenius , illuminates the phylogeography and
`evolution of cattle , ” Genome Biology 16 : 234 ( 2015 ) .
`Park et al . , “ Generation of germline ablated male pigs by CRISPR /
`Cas9 editing of the NANOS2 gene , ” Scientific Reports ( 2017 ) .
`Ross et al . , “ Bovine Somatic Cell Nuclear Transfer , " Methods Mol
`Biol . 636. 155-77 ( 2010 ) .
`Schefers et al . , " Genomic selection in dairy cattle : Integration of
`DNA testing into breeding programs , ” Animal Frontiers 2 ( 1 ) : 1-9
`( 2012 ) .
`The Holstein Association USA ( HAU ) downloaded from
`www ( dot ) holsteinusa ( dot ) com / genetic_evaluations / ss_tpi_formula .
`htmlMar . 28 , 2019 .
`( Continued )
`Primary Examiner Marcia S Noble
`( 74 ) Attorney , Agent , or Firm — Elizabeth A. Epstein ;
`Michael Stimson
`ABSTRACT
`( 57 )
`The disclosure relates to Bovine germplasm of Bos taurus
`variety HO840M003150607238 . Included in the present
`disclosure are cells comprising the genome of Bovine vari
`ety HO840M003150607238 characterized by the presence
`of homozygous loci and spermatozoa obtained from said
`cells . Also provided by the present disclosure are tissue
`cultures of cells , animals obtained from said cells , and parts
`thereof , including F1 spermatozoa . The disclosure further
`provides for methods of breeding , selecting , and using the
`germplasm to improve existing commercial cattle herds
`generated from in vitro fertilization methods and progeny
`cattle obtained from in vitro fertilization and implantation
`and artificial insemination methods .
`22 Claims , No Drawings
`Specification includes a Sequence Listing .
`
`( 51 )
`
`( 52 )
`
`( 58 )
`
`( 56 )
`
`Int . Cl .
`C12N 5/0735
`A01K 677027
`C12N 5/076
`C12N 57075
`C12N 15/877
`U.S. CI .
`CPC
`
`( 2010.01 )
`( 2006.01 )
`( 2010.01 )
`( 2010.01 )
`( 2010.01 )
`
`C12N 5/0611 ( 2013.01 ) ; A01K 67/027
`( 2013.01 ) ; C12N 5/061 ( 2013.01 ) ; C12N
`5/0609 ( 2013.01 ) ; C12N 15/8771 ( 2013.01 ) ;
`A01K 2227/101 ( 2013.01 )
`Field of Classification Search
`CPC
`C12N 5/061 ; C12N 5/0611 ; C12N 5/0609 ;
`C12N 5/06 ; A01K 67/027 ; A01K
`2227/101
`See application file for complete search history .
`References Cited
`U.S. PATENT DOCUMENTS
`6,011,197 A
`1/2000 Strelchenko et al .
`1/2018 May et al .
`9,868,962 B2
`2003/0157475 A1
`8/2003 Schenk
`
`FOREIGN PATENT DOCUMENTS
`
`WO
`WO
`
`WO 2015/148761
`WO 2017/132239
`
`10/2015
`8/2017
`
`OTHER PUBLICATIONS
`Printout from plant variety | InforMEA . https://www.informea.org
`en / terms / plant - variety . Printed Jan. 8 , 2020. pp . 3 of ( Year : 2020 ) . *
`Hinch et al . Science 363 , 1300 ( 2019 ) pp . 1-10 ( Year : 2019 ) . *
`Bovine HapMap Consortium data set ( Bovine HapMap Consortium ,
`“ Genome - wide survey of SNP variation uncovers the genetic struc
`ture of cattle breeds , ” Science 324 ( 5926 ) : 528-32 ( 2009 ) .
`Burkard et al . , “ Precision engineering for PRRSV resistance in pigs :
`Macrophages from genome edited pigs lacking CD 163 SRCR5
`domain are fully resistant to both PRRSV genotypes while main
`taining biological function , ” PLOS Pathogens 13 ( 2 ) ( 2017 ) .
`Cole et al . , “ Haplotype tests for recessive disorders that affect
`fertility and other traits , " USDA AIP Research Report Genomic3
`
`Exhibit 1001
`Select Sires, et al. v. ABS Global
`
`

`

`US 10,982,187 B2
`Page 2
`
`( 56 )
`
`References Cited
`
`OTHER PUBLICATIONS
`VanRaden et al . , “ Genetic Evaluation of Length of Productive Life
`Including Predicted Longevity of Live Cows , ” Journal of Dairy
`Science 76 : 2758-2764 ( 1993 ) .
`VanRaden et al . ,
`“ Productive Life Evaluations : Calculation , Accu
`racy , and Economic Value , " Journal of Dairy Science 78 : 631-638
`( 1995 ) .
`VanRaden et al . , “ Methods used to compute multi - trait productive
`life , ” USDA AIPL Research Report PLC ( Nov. 2003 ) ( 2003 ) .
`VanRaden et al . , “ Net merit as a measure of lifetime profit : 2018
`revision , ” USDA AIP Research Report NM $ 7 ( May 2018 ) ( 2018 ) .
`Weigel et al . , “ Use of Linear Type and Production Data to Supple
`ment Early Predicted Transmitting Abilities for Productive Life , ”
`Journal of Dairy Science 81 : 2040-2044 ( 1998 ) .
`Worley , Bovine Genome Sequencing and Analysis Consortium .
`“ The genome sequence of taurine cattle : a window to ruminant
`biology and evolution , ” Science 324 ( 5926 ) : 522-8 ( 2009 ) .
`Whitworth et al . ,
`“ Use of the CRISPR / Cas9 System to Produce
`Genetically Engineered Pigs from In Vitro - Derived Oocytes and
`Embryos , ” Biology of Reproduction 91 ( 3 ) : 78 ( 2014 ) .
`Allen A.R. , et al . , 2010 , Compilation of a panel of informative
`single nucleotide polymorphisms for bovine identification in the
`Northern Irish cattle population . BMC Genetics 2010 , 11 : 5 .
`* cited by examiner
`
`Exhibit 1001
`Select Sires, et al. v. ABS Global
`
`

`

`US 10,982,187 B2
`
`1
`2
`BOS TAURUS VARIETY ' HO840003150607238 '
`having at least 90 % of the nucleic acid sequences selected
`from the group consisting of SEQ ID NOs : 1 to 29048 .
`AND METHODS OF USE THEREOF
`The present disclosure provides for , and includes , a plu
`INCORPORATION OF SEQUENCE LISTING
`rality of Bos taurus gamete cells comprising at least 90 % of
`5 the loci comprising the nucleic acid sequences selected from
`The Sequence Listing is hereby incorporated by reference
`the group consisting of SEQ ID NOs : 1 to 29048 .
`In an aspect , the present disclosure includes , and provides
`in its entirety , including the file named P34675_ST25.txt ,
`which is 47,645,133 bytes in size and was created on Mar.
`for , an F1 Bos taurus animal , or part thereof , said F1 Bos
`26 , 2019 , which is likewise herein incorporated by reference
`taurus animal comprising a genome comprising at least 90 %
`10 of the loci comprising the nucleic acid sequences selected
`in its entirety .
`from the group consisting of SEQ ID NOs : 1 to 29048 .
`In another aspect , the present disclosure provides for , and
`FIELD OF THE INVENTION
`includes , an F1 Bos taurus animal , or part thereof , compris
`The present disclosure relates to the field of Bos taurus
`ing a genome comprising at least 90 % of the loci comprising
`breeding . In particular , the present disclosure related to Bos 15 the nucleic acid sequences selected from the group consist
`taurus variety HO840003150607238 having high multi - trait
`ing of SEQ ID NOs : 1 to 29048 .
`In a further aspect , the present disclosure provides for , and
`selection indices and high trait transmissibility .
`includes a Bos taurus animal , or part thereof , comprising one
`or more cells having at least 25 % of the loci comprising
`BACKGROUND OF THE INVENTION
`20 nucleic acid sequences selected from the group consisting of
`SEQ ID NOs : 1 to 29048 .
`There are numerous steps in the development of any new ,
`An even further aspect of the present disclosure is a
`desirable Bos taurus germplasm . Bos taurus breeding begins
`plurality of Bos taurus cells , each comprising a diploid or
`with the analysis and definition of problems and weaknesses
`haploid genome each diploid genome comprising homozy
`of the current germplasm , the establishment of program
`goals , and the definition of specific breeding objectives . The 25 gous loci comprising at least 90 % of the nucleic acid
`next step is selection of germplasm that possess the traits to
`sequences selected from the group consisting of SEQ ID
`meet the program goals . A goal is to combine in a single
`NOs : 1 to 29048 ; and each haploid genome comprising at
`variety an improved combination of desirable traits from the
`least 90 % of the loci comprising the nucleic acid sequences
`parental germplasm . See Schefers et al . , “ Genomic selection
`selected from the group consisting of SEQ ID NOs : 1 to
`in dairy cattle : Integration of DNA testing into breeding 30 29048 .
`programs ” Animal Frontiers 2 ( 1 ) : 1-9 ( 2012 ) .
`During breeding , cattle breeders have a variety of sources
`DETAILED DESCRIPTION
`when making breeding decisions . In addition to genomic
`A goal of a Bos taurus breeding program is to combine in
`data , a number of agencies and organizations collect and
`release analysis of population data and indexes . Every three 35 a single Bos taurus variety an improved combination of
`months , the Animal Improvement Programs Laboratory
`desirable traits from the parental germplasm that provides
`( AIPL ) of the United States Department of Agriculture
`for desirable progeny when used in artificial insemination
`and in vitro fertilization programs . Improved Bos taurus
`releases the newest USDA - DHIA ( Dairy Herd Improvement
`Association ) genetic evaluations for dairy bulls and cows .
`inseminate varieties are useful for various artificial breeding
`The AIPL calculates genetic evaluations for type for various 40 techniques , including artificial insemination ( “ AI ” ) and
`breeds , and many breed associations provide their own
`embryo transfer ( “ ET ” ) . Improved Bos taurus germplasm ,
`indexes or other strategies for evaluating certain breed-
`varieties , and inseminates prepared therefrom , are desirable .
`relevant traits . U.S. dairy genetic evaluations are computed
`The present disclosure provides for , and includes , an
`every four months by the Council on Dairy Cattle Breeding
`improved elite SM germplasm obtained from a multigen
`( CDCB ) and Holstein Association USA ( HAU ) . Both CDCB 45 erational breeding program . The germplasm is unique and
`and HAU traits provide the breeder within important com-
`readily distinguishable from germplasm present in non
`parative data to evaluate the complex genetic and pheno-
`selected cattle . Indeed , in the absence of continued selection ,
`typic traits to develop improved and desirable Bos taurus
`the germplasm reverts to heterogeneity and diversity . As
`germplasm . For Holstein and Jersey sires , for example ,
`provided herein , the germplasm of the present disclosure is
`evaluations are genomically enhanced and represent a blend- 50 identifiable using standard methods and the germplasm can
`ing of genomic data , pedigree information , and results from
`be readily identified in progeny generations . Indeed , as few
`progeny . These genetic evaluations provide the breeder
`as 800 SNP markers are sufficient to identify parentage with
`important information for the selection of desirable germ-
`greater than 99 % accuracy . See McClure et al . , " SNP Data
`plasm and the development of new and valuable insemi-
`Quality Control in a National Beef and Dairy Cattle System
`55 and Highly Accurate SNP Based Parentage Verification and
`nates .
`There is a continuous need to develop improved Bos
`Identification , ” Frontiers in Genetics 9 ( 84 ) : 1-14 ( 2018 ) . As
`provided here , the tens of thousands of sequences provide
`taurus germplasm for use in improving production herds as
`well as for the continued improvement of elite animals . The
`for tracking and selecting animals through multiple genera
`present germplasm is the result of crosses between superior
`tions . Breeding with the germplasm provided herein , com
`elite females ranked by performance as among the top 1 % of 60 bined with the selection of suitable mates will maintain the
`the population of domesticated dams and elite bulls that are
`desirable germplasm in subsequent generations . Moreover ,
`genetic testing allows for the removal of progeny having
`among the top 5 % of the domestic population .
`germplasm that lacks that set of desired loci for the improve
`ment of cattle herds .
`SUMMARY OF THE INVENTION
`The present disclosure provides for , and includes , cells ,
`animals ,
`and progeny
`The present disclosure comprises , in one form thereof , a
`Bos taurus
`variety
`of
`HO840003150607238 ( “ Animal ” ) comprising an improved
`plurality of Bos taurus cells each cell comprising a genome
`
`65
`
`Exhibit 1001
`Select Sires, et al. v. ABS Global
`
`

`

`US 10,982,187 B2
`
`TABLE 1
`
`Genotype of Bos taurus animal HO840003150607238 ( “ Animal ” )
`SEQ ID Range
`No. of
`Alternate
`SEQ ID NOs : 1 to 29048
`Alleles
`
`Reference Allele
`
`Alternate Allele
`
`3
`4
`The present disclosure provides for , and includes , a dip
`germplasm characterized by SEQ ID NOs : 1 to 41648 and
`loid Bos taurus cell or a plurality of diploid Bos taurus cells
`homozygous loci comprising the nucleic acid sequences
`comprising improved germplasm characterized by a genome
`selected from the group consisting of SEQ ID NOs : 1 to
`having homozygous loci comprising 90 % to 100 % of the
`29048 , and listed in Table 1. Animal differs from the
`reference genome at 11832 homozygous loci , or about 28 % 5 nucleic acid sequences selected from the group consisting of
`SEQ ID NOs : 1 to 29048 .
`of the total loci .
`Animal is the progeny of a cross between Sire
`HO840003135669665
`( “ Sire ” )
`and
`Dam
`HO840003128557405 ( “ Dam ” ) . The genotype of Sire is
`10 represented by the SEQ ID NOs : 41649 to 82185 and
`homozygous loci comprising the nucleic acid sequences
`selected from the group consisting of SEQ ID NOs : 41649
`to 68810 and listed in Table 2 ( " Sire Genotype ” ) . Sire differs
`from the reference genome at 10935 homozygous loci , or
`15 about 27 % of the total loci .
`
`Homozygous
`
`Chromosome 1
`Chr . 2
`Chr . 3
`Chr . 4
`Chr . 5
`Chr . 6
`Chr . 7
`Chr . 8
`Chr . 9
`Chr . 10
`Chr . 11
`Chr . 12
`Chr . 13
`Chr . 14
`Chr . 15
`Chr . 16
`Chr . 17
`Chr . 18
`Chr . 19
`Chr . 20
`Chr . 21
`Chr . 22
`Chr . 23
`Chr . 24
`Chr . 25
`Chr . 26
`Chr . 27
`Chr . 28
`Chr . 29
`
`1-1110
`1111-01954
`1955-2883
`2884-3684
`3685-4439
`4440-5272
`5273-5962
`5963-6797
`6798-7455
`7456-8125
`8126-8809
`8810-9358
`9359-9951
`9952-10592
`10593-11148
`11149-11703
`11704-12314
`12315-12797
`12798-13309
`13310-13823
`13824-14279
`14280-14702
`14703-15016
`15017-15414
`15415-15770
`15771-16151
`16152-16444
`16445-16812
`16813-17187
`
`Heterozygous
`
`SEQ ID Range
`
`Chromosome 1
`Chr . 2
`Chr . 3
`Chr . 4
`Chr . 5
`Chr . 6
`Chr . 7
`Chr . 8
`Chr . 9
`Chr . 10
`Chr . 11
`Chr . 12
`Chr . 13
`Chr . 14
`Chr . 15
`Chr . 16
`Chr . 17
`Chr . 18
`Chr . 19
`Chr . 20
`Chr . 21
`Chr . 22
`Chr . 23
`Chr . 24
`Chr . 25
`Chr . 26
`Chr . 27
`Chr . 28
`Chr . 29
`
`29049-29832
`29833-30576
`30577-31069
`31070-31789
`31790-32326
`32327-32899
`32900-33505
`33506-34086
`34087-34609
`34610-35231
`35232-35844
`35845-36305
`36306-36749
`36750-36970
`36971-37461
`37462-37865
`37866-38181
`38182-38494
`38495-38763
`38764-39143
`39144-39454
`39455-39787
`39788-40099
`40100-40457
`40458-40689
`40690-40949
`40950-41236
`41237-41401
`41402-41648
`
`17188-17963
`17964-18580
`18581-19199
`19200-19689
`19690-20169
`20170-20823
`20824-21347
`21348-21843
`21844-22309
`22310-22775
`22776-23290
`23291-23663
`23664-24058
`24059-24647
`24648-24987
`24988-25348
`25349-25729
`25730-26027
`26028-26360
`26361-26736
`26737-27082
`27083-27360
`27361-27615
`27616-27882
`27883-28107
`28108-28362
`28363-28574
`28575-28812
`28813-29048
`No. Alternate
`alleles
`
`775
`616
`618
`489
`479
`653
`523
`495
`465
`465
`514
`372
`394
`588
`339
`360
`380
`297
`332
`375
`345
`277
`254
`266
`224
`254
`211
`237
`235
`11832
`
`20
`
`TABLE 2
`Genotype of Sire HO840003135669665 ( Sire Genotype )
`SEQ ID Range
`No. of
`Alternate
`SEQ ID NOs : 41649-68810
`Reference Allele
`Alternate Allele
`Alleles
`754
`41649-42719
`57847-58601
`557
`42720-43499
`58602-59159
`623
`43500-44453
`59160-59783
`59784-60266
`44454-45260
`482
`45261-45934
`60267-60700
`433
`564
`459345-46671
`60701-61265
`46672-47422
`61266-61885
`619
`47423-48224
`61886-62406
`520
`48225-48890
`62407-62852
`445
`456
`48891-49556
`62853-63309
`507
`49557-50233
`63310-63817
`63818-64185
`367
`50234-50737
`64186-64534
`50738-51301
`348
`469
`51302-51833
`64535-65004
`65005-65353
`348
`51834-52378
`52379-52865
`65354-65668
`314
`52866-53404
`65669-65967
`298
`53405-53798
`65968-66197
`229
`66198-66464
`266
`53799-54206
`54207-54696
`66465-66813
`348
`54697-55109
`66814-67072
`258
`55110-55539
`67073-67329
`256
`235
`55540-55826
`67330-67565
`67566-67821
`55827-56213
`255
`56214-56566
`67822-68028
`206
`56567-56940
`68029-68274
`245
`56941-57230
`68275-68477
`202
`57231-57518
`68478-68648
`170
`57519-57846
`161
`68649-68810
`No. Alternate
`10935
`alleles
`
`Homozygous
`Chromosome 1
`25 Chr . 2
`Chr . 3
`Chr . 4
`Chr . 5
`Chr . 6
`Chr . 7
`30 Chr . 8
`Chr . 9
`Chr . 10
`Chr . 11
`Chr . 12
`Chr . 13
`35 Chr . 14
`Chr . 15
`Chr . 16
`Chr . 17
`Chr . 18
`Chr . 19
`Chr . 20
`Chr . 21
`Chr . 22
`Chr . 23
`Chr . 24
`Chr . 25
`Chr . 26
`45 Chr . 27
`Chr . 28
`Chr . 29
`
`40
`
`50
`
`Heterozygous
`Chromosome 1
`Chr . 2
`Chr . 3
`55 Chr . 4
`Chr . 5
`Chr . 6
`Chr . 7
`Chr . 8
`Chr . 9
`Chr . 10
`Chr . 11
`Chr . 12
`Chr . 13
`Chr . 14
`Chr . 15
`Chr . 16
`65 Chr . 17
`Chr . 18
`
`60
`
`SEQ ID Range
`
`68811-82185
`68811-69568
`69569-70363
`70364-70760
`70761-71423
`71424-72041
`72042-72719
`72720-73111
`73112-73656
`73657-74158
`74159-74759
`74760-75333
`75334-75787
`75788-76276
`76277-76695
`76696-77157
`77158-77633
`77634-78084
`78085-78534
`
`Exhibit 1001
`Select Sires, et al. v. ABS Global
`
`

`

`US 10,982,187 B2
`
`5
`TABLE 2 - continued
`Genotype of Sire HO840003135669665 ( Sire Genotype )
`78535-78953
`78954-79354
`79355-79764
`79765-80082
`80083-80419
`80420-80769
`80770-81008
`81009-81269
`81270-81548
`81549-81839
`81840-82185
`
`Chr . 19
`Chr . 20
`Chr . 21
`Chr . 22
`Chr . 23
`Chr . 24
`Chr . 25
`Chr . 26
`Chr . 27
`Chr . 28
`Chr . 29
`
`5
`
`6
`TABLE 3 - continued
`Genotype of Dam H0840003128557405 ( “ Dam Genotype ” )
`Chr . 13
`117066-117610
`Chr . 14
`117611-117973
`Chr . 15
`117974-118467
`Chr . 16
`118468-118832
`118833-119198
`Chr . 17
`Chr . 18
`119199-119559
`119560-119828
`Chr . 19
`10 Chr . 20
`119829-120190
`Chr . 21
`120191-120554
`120555-120841
`Chr . 22
`Chr . 23
`120842-121068
`121069-121323
`Chr . 24
`121324-121625
`Chr . 25
`121626-121970
`Chr . 26
`121971-122194
`Chr . 27
`122195-122406
`Chr . 28
`Chr . 29
`122407-122589
`
`15
`
`The genotype of Dam is represented by the SEQ ID NOs :
`82186-122589 and homozygous loci comprising the nucleic
`acid sequences selected from the group consisting of SEQ
`ID NOs : 82186 to 98686 and listed in Table 3 ( “ Dam
`Genotype ” ) . Dam differs from the reference genome at
`11237 homozygous loci , or about 28 % of the total loci .
`TABLE 3
`Genotype of Dam H0840003128557405 ( “ Dam Genotype ” )
`SEQ ID Range
`No. of
`SEQ ID NOs : 82186-98686
`Alternate
`
`20
`
`25
`
`Notably , and as expected for a select cross between Sire
`and Dam , the number of homozygous alleles in Animal
`increases compared to both parents . As show in Table 4 ,
`Animal retains 70 to 80 % of the homozygous alleles found
`in Sire and Dam and more than 15 % of the heterozygous
`alleles in Sire and Dam are fixed as homozygous in Animal .
`These results demonstrate that improvements by selective
`are breeding are reflected in the germplasm and that such
`improvements do not require , but may be informed by , a
`priori knowledge of the genotype of the germplasm .
`
`Homozygous
`
`Chromosome 1
`Chr . 2
`Chr . 3
`Chr . 4
`Chr . 5
`Chr . 6
`Chr . 7
`Chr . 8
`Chr . 9
`Chr . 10
`Chr . 11
`Chr . 12
`Chr . 13
`Chr . 14
`Chr . 15
`Chr . 16
`Chr . 17
`Chr . 18
`Chr . 19
`Chr . 20
`Chr . 21
`Chr . 22
`Chr . 23
`Chr . 24
`Chr . 25
`Chr . 26
`Chr . 27
`Chr . 28
`Chr . 29
`
`Heterozygous
`Chromosome 1
`Chr . 2
`Chr . 3
`Chr . 4
`Chr . 5
`Chr . 6
`Chr . 7
`Chr . 8
`Chr . 9
`Chr . 10
`Chr . 11
`Chr . 12
`
`Reference Allele
`
`Alternate Allele
`
`Alleles
`
`82186-83192
`83193-84062
`84063-84881
`84882-85725
`85726-86405
`86406-87219
`87220-87869
`87870-88653
`88654-89284
`89285-89899
`89900-90666
`90667-91210
`91211-91734
`91735-92282
`92283-92836
`92837-93376
`93377-93940
`93941-94380
`94381-94873
`94874-95367
`95368-95770
`95771-96219
`96220-96562
`96563-96993
`96994-97303
`97304-97640
`97641-97962
`97963-98283
`98284-98686
`
`98687-99371
`99372-99977
`99978-100492
`100493-101051
`101052-101490
`101491-102080
`102081-102587
`102588-103065
`103066-103516
`103517-103940
`103941-104564
`104565-104932
`104933-105256
`105257-105760
`105761-106060
`106061-106423
`106424-106775
`106776-107030
`107031-107351
`107352-107726
`107727-108041
`108042-108305
`108306-108588
`108589-108894
`108895-109070
`109071-109263
`109264-109489
`109490-109703
`109704-109952
`No. Alternate
`alleles
`
`754
`557
`623
`482
`433
`564
`619
`520
`445
`456
`507
`367
`348
`469
`348
`314
`298
`229
`266
`348
`258
`256
`235
`255
`206
`245
`202
`170
`161
`11237
`
`SEQ ID Range
`
`109953-122589
`109953-110857
`110858-111511
`111512-112144
`112145-112680
`112681-113278
`113279-113859
`113860-114455
`114456-115061
`115062-115588
`115589-116273
`116274-116642
`116643-117065
`
`30
`
`35
`
`TABLE 4
`
`Select cross increases homozygosity
`Homozygous
`Matches
`from parent
`
`Just
`Parent type
`
`Alleles
`
`Sire
`
`Dam Admiral
`
`S % D % S % D %
`
`Homo ref
`Homo alt
`40 Homo
`homo
`Het to
`homo
`
`12944
`8663
`21607
`
`13040
`8313
`21353
`
`17187
`11832
`29048
`
`32 %
`21 %
`54 %
`
`32 %
`21 %
`53 %
`
`80 %
`79 %
`80 %
`
`79 %
`74 %
`77 %
`
`6724
`
`6340
`
`17 % 16 % 50 % 50 %
`
`45
`
`50
`
`It is to be understood that the disclosure is not necessarily
`limited in its application to the details set forth in the
`following description or exemplified by the Examples . The
`disclosure is capable of other aspects or of being practiced
`or carried out in various ways .
`As used herein the term “ about ” refers to + 10 % .
`As used herein , the singular forms “ a , ” “ an , ” and “ the ”
`include plural references unless the context clearly dictates
`otherwise . For example , the term “ a compound ” or “ at least
`one compound ” may include a plurality of compounds ,
`55 including mixtures thereof
`Throughout this application , various embodiments of this
`disclosure may be presented in a range format . It should be
`understood that the description in range format is merely for
`convenience and brevity and should not be construed as an
`60 inflexible limitation on the scope of the disclosure . Accord
`ingly , the description of a range should be considered to
`have specifically disclosed all the possible subranges as well
`as individual numerical values within that range . For
`example , description of a range such as “ from 1 to 6 " should
`65 be considered to have specifically disclosed subranges such
`as " from 1 to 3 , " " from 1 to 4 , " " from 1 to 5 , " " from 2 to
`4 , ” “ from 2 to 6 , " " from 3 to 6 , ” etc. , as well as individual
`
`Exhibit 1001
`Select Sires, et al. v. ABS Global
`
`

`

`US 10,982,187 B2
`
`7
`8
`gosity is maintained when the second parent is an elite
`numbers within that range , for example , 1 , 2 , 3 , 4 , 5 , and 6 .
`This applies regardless of the breadth of the range .
`parent with high trait values as described below . Similarly ,
`the improved germplasm of the present disclosure can be
`Whenever a numerical range is indicated herein , it is
`maintained by selecting superior breeding partners in the F1
`meant to include any cited numeral ( fractional or integral )
`within the indicated range . The phrases “ ranging / ranges 5 and later progeny generations . By suitable selection of the
`between ” a first indicate number and a second indicate
`second parent , the germplasm can be maintained at the
`number and “ ranging / ranges from ” a first indicate number
`homozygous loci . Even further , careful selection of elite
`“ to ” a second indicate number are used herein interchange-
`breeding partners results increased numbers of homozygous
`ably and are meant to include the first and second indicated
`loci as the preferred allele at the heterozygous loci are
`numbers and all the fractional and integral numerals there 10 homozygosed in elite progeny . Notably , knowledge of the
`underlying biology is helpful , but not required .
`between .
`For the purposes of this invention the term " semen ”
`As used herein , “ gamete ” refers to a haploid germ cell and
`includes either a sperm or an ovum and may be used
`means seminal fluid which may contain sperm ( also referred
`to as “ spermatozoa " ) secreted by the gonads of a male
`interchangeably . Generally , the identity as a sperm or an
`animal which can be collected from the male animal by a 15 ovum can be determined by the context as bulls produced
`variety of methods such as use of an artificial vagina , manual
`sperm and dams produce ova . For the purposes of this
`manipulation of the penis , electrical manipulation of the
`invention the term " sperm ” means the haploid cell that is the
`gamete of a male animal which may join an egg ( also
`anus , or the like .
`As used herein , “ locus " , or plural “ loci ” , refers to a
`referred to as " ovum ” ) to produce a zygote and broadly
`physical site or location of a specific gene or marker on a 20 encompasses infertile sperm , sperm having a comparably
`chromosome . Loci of the present disclosure include , and are
`lesser or a comparably greater fertility between a first
`identifiable by , a SEQ ID NO , each SEQ ID NO providing
`amount of sperm obtained from a first animal and a second
`the identity of the polymorphism at a single nucleotide
`amount of sperm obtained from a second animal and which
`polymorphic site and the adjacent 100 base pairs .
`may be obtained in the form of a raw ejaculated semen ,
`Loci may also characterized as either ‘ A ’ loci , ‘ B ' loci , or 25 frozen semen , as sperm separated from the semen and
`heterozygous ‘ A / B ' loci . The identification of loci as either
`contained in an extender or diluent , or as sex - selected sperm .
`‘ A’or ‘ B ' loci is determined according to the top ( TOP ) and
`As used herein , the term " inseminate ” is intended to
`bottom ( BOT ) designations based on the polymorphism
`broadly encompass an amount of sperm whether contained
`itself , or the contextual surrounding sequence as developed
`in semen together with a cryoprotectant . Inseminates may
`by Illumina . Methods for determining the designation of a 30 optionally include one or more “ extenders ” and diluents
`polymorphic site as ‘ A ’ or ‘ B ’ are known in the art , for
`which can be utilized to fertilize the eggs of a female animal
`example as provided by Illumina's Technical Note entitled
`whether in vitro or in vivo . As used herein , inseminates can
`“ TOP / BOT Strand and ‘ A / B'Allele ” , available on the
`further include sex - selected sperm compositions .
`internet at www ( dot ) illumina ( dot ) com / documents / products /
`As used herein , the term “ sex - selected sperm ” means
`technotes / technote_topbot.pdf . The NCBI's dbSNP data- 35 sperm which have been separated , regardless as to the
`base has adopted the TOP / BOT nomenclature in 2005 and
`method of separation , into subpopulations containing
`the designation is well known to those of skill in the art . As
`X - chromosome bearing sperm and Y - chromosome bearing
`shown in the Examples , through sequence comparison
`sperm having a purity in the range of about 70 percent ( " % " )
`extensive information about each loci is available to a
`and about 100 % .
`person of ordinary skill in the art , including , but not limited 40
`Predicted Transmitting Abilities ( PTAs ) can be computed
`to , dbSNP identifier , sources , chromosomal location , genes ,
`for various traits , for example in the broad categories of
`transcripts , linkage to genes or quantitative trait loci ( QTL ) ,
`production ( milk and milk components ) , health / fitness , and
`type . Dairy cattle are evaluated for the traits of milk , fat , and
`and interactions .
`As used herein , “ germplasm ” means an intact genome
`protein yield , length of productive life , and somatic cell
`present in cells or nuclei and comprising chromosomes . In 45 score ( an indicator of mastitis ) . Evaluation procedures com
`diploid cells , the germplasm is characterized by the presence
`bine information from relatives of an evaluated animal , and
`of sequences representing the sequences at polymorphic
`from the animal itself in the case of cows . Additionally ,
`sites ( e.g. , SNPs ) that are homozygous or heterozygous . As
`numerous type or conformation traits are evaluated rou
`used herein , the germplasm of the present disclosure is
`tinely .
`characterized by the homozygous loci . In haploid cells ( e.g. , 50
`An important aspect of Bos taurus breeding programs are
`ova or sperm ) , the each of the sequences at each homozy-
`genetic values for yield , management traits , and type that are
`gous loci in the parent are present in each cell . In contrast ,
`reported as PTAs . These important traits include higher
`heterozygous loci are present in haploid germplasm accord-
`milk , protein and fat yield PTAs shown as added pounds of
`ing to random assortment . Accordingly , the genotype at
`milk , fat , and protein expected per lactation for average
`heterozygous loci in haploid cells varies from haploid cell to 55 daughters of individual sires . PTAs are also expressed as
`haploid cell , while the sequences of the homozygous loci
`percentage traits that are represented as percentage point
`from the parent are present in each haploid cell and are
`differences where plus values indicate higher concentration
`therefore faithfully transmitted to progeny .
`of fat and protein in milk . Bos taurus animals and cells
`During breeding , to maintain and improve the germplasm ,
`obtained therefrom are also selected to provide increased
`selections of a second parent may be an elite second parent 60 numbers of daughters and herds contributing to production ,
`having superior traits . As demonstrated in the examples ,
`improved reliability , improved productive life , improved
`such select crosses result in progeny that retain significant
`somatic cell score ( SCS ) . Desirable Bos taurus varieties
`numbers of homozygous loci present in each elite parent and
`provide higher daughter pregnancy rates ( DPR ) that are a
`further result in additional loci becoming homozygous .
`genetic measure of the percentage of non - pregnant cows that
`Thus , select crosses result in some or all of the homozygous 65 become pregnant during each 21 - day period ( heat cycle ) .
`loci of the Bos taurus cells of the present disclosure being
`Another important and desirable PTA selected by breeders is
`retained in progeny generations . Generally , locus homozy-
`the