CENTRE OF ADVANCED FACULTY TRAINING
(Animal Genetics and Breeding)
DAIRY CATTLE BREEDING DIVISION
NATIONAL DAIRY RESEARCH INSTITUTE
KARNAL-132001 (HARYANA), INDIA
Dated: 14th Feb., 2013
Dr. R. S. Gandhi
Director CAFT in Animal Genetics and Breeding &
Head DCB Division
Subject: Proposal for training programme & request for release of budget under CAFT 2013-14.
Dear Dr. Sharma,
With reference to your letters No. 1 (37)/CAFTs-2013/HRD dated 08th February, 2013,
following training program is being proposed during 2013-14. Kindly find enclosed title and
topic to be covered under the 21 days training programme of CAFT.
You are requested to release budget for smoothly conducting the training programme and other
related activities of CAFT.
It is further informed that a total of 17 participants participated in the training program entitled
“Advanced Statistical Tools for Analysis of Animal Breeding Data held during March 10-30,
2012.
Submitted for your kind consideration and perusal, please.
With Best Regards,
(R. S. Gandhi)
Dr. K. Sharma
Assistant Director General (HRD) &
Controller of Examinations (Edn)
Education Division,
ICAR, Krishi Anusandhan Bhavan II,
PUSA, New Delhi-110012
E-mail: ravindersinghgandhi@gmail.com
Phone: 0184 2259094; 09896697700;
Fax: 0184 2250042
1. Topic of Training Programme
Advanced Breeding
Productivity
and
Allied
Technologies
for
Enhancing
Livestock
2 Justification of the Proposed Program:
It has been observed over the years that the conventional strategies for the
improvement of livestock productivity required more time. Many advanced breedingmanagement technologies including novel cytogenetic and molecular breeding
technologies, genetic resistance to diseases of livestock, have emerged in the last two
decades, which have the potential for enhancing the productivity of livestock in a shorter
period of time. The proposed training program will extensively cover the basic concepts
and methodologies of all the breeding and related frontier areas. The training program
will also focus on application of advanced breeding and allied technologies in organized
and unorganized herds, their economic feasibility and the time required for
standardization and adoption as well as infrastructure needed for genetic improvement
of livestock in the diverse conditions in our country.
3. Venue:
Centre of Advanced Faculty Training, Dairy Cattle Breeding Division, NDRI, Karnal132001, Haryana, India
Phone: 0184-2259092[O], 098966-97700[M]; Fax : 0184-2250042
E-mail: ravindersinghgandhi@gmail.com
4. Proposed dates: March 05 - 25, 2014
5. Eligibility qualification for the participants of the Training Program:
i ) Master’s Degree
ii) Working not below the rank of Assistant Professor and equivalent in the concerned
and related subjects under State Agricultural/ Veterinary University and ICAR
institutes.
6. Information regarding proposed Course Coordinator:
i). Name of Course Coordinator
Prof. ( Dr ) A. K. Chakravarty
ii). Designation
Principal Scientist & In-charge,
Artificial Breeding Research Center
National Dairy Research Institute
Karnal-132001, Haryana, India
iii). Specific Qualification
iv). Area of Specialization:
M.V.Sc (Animal Genetics & Breeding )
Ph.D (Animal Genetics & Breeding )
Animal Genetics & Breeding / Livestock
Breed Improvement.
v). Experience and Scientific Contributions
The scientist, a Founder Fellow of National Academy of Dairy Science, is engaged over
26 years in research and extension program, developed animal breeding technologies
and significantly contributed in dairy animal improvement program in the country. The
scientist has more than 23 years of teaching experience for M.Sc / M.V.Sc/ Ph.D
students of Animal Genetics and Breeding, Livestock Production and Management. The
scientist designed and developed various courses for post graduate programs. As
Program Coordinator, the scientist organized Three 21 days National Training programs
under Centre for Advanced Studies (CAS) in Animal Genetics & Breeding and also
acted as joint coordinator and designed the courses for National Training Program
under CAS, in Animal Genetics & Breeding at NDRI, Karnal. The Scientist taught the
trainees in many National Training Programs and in other universities. As a Major
Guide,the scientist guided seventeen M.Sc / M.V.Sc and Ph.D students. The scientist
was awarded national fellowship and the leading achievers Who's Who World-2010
award from around the globe based on scientific contribution and life-long
achievements.
7. Faculty Staff Strength in CAFT (Animal Genetics & Breeding):
Dr. R.S.Gandhi, Head
Dr. G.K.Sachdeva, PS
Dr.B.R.Yadav,PS
Dr. A.K.Gupta, PS
Dr. A.K.Chakravarty, PS
Dr. Archana Verma, PS
Dr.I.D.Gupta, PS
Dr.Avtar Singh, PS
8. Information regarding other academic staff of the host institute:
The faculty of related divisions of the NDRI, the scientists of NBAGR and the invited
experts on the proposed topic from reputed institutes are to be used as resource
persons for conducting the training program. Besides this, guest faculty from IASRI,
New Delhi; PDC Meerut; CIRB Hisar & IVRI, Bareilly will also be invited.
9. Availability of Specific facilities:
All kind of facilities and infrastructure are available at the DCB Division and in the
institute for conducting the training program.
10. Programs/ Projects and achievements in the area of special topic proposed
for the training program:
(For details kindly see Annexure – I)
11. Schedule of lectures and practical topics to be covered:
To be decided in due course of time
12. Name of the training organized during the last three years:
1. Advances in Breeding and Management Technology for Improvement in
Livestock Productivity (25 March-14 April 2009).
2. Databases and Softwares for Analysis of Animal Genetic and Breeding Data (1030 March, 2011).
3. Advanced Statistical Tools for Analysis of Animal Breeding Data (March 10 - 30
2012)
13. Signature of the Director, CAFT (AG&B)
Annexure – I
Project 1: Integrated genetic improvement of dairy cattle and buffaloes under open
nucleus breeding system
Achievements:

A total of 119 KF, 78 Sahiwal and 80 Murrah young males have been reserved for
progeny testing during the project period (2007-2011). The ranges for the expected
predicted difference (EPD %) and dam’s best 305-day milk yields for the three breeds
were 1.57-18.44, 0.24-23.10 and 1.69-18.63% and 4546-8648, 1906-3811 and 23304341 kg, respectively.

The proportion of the elite herd had a range of 23-41% in Karan Fries, 21-26% in
Sahiwal and 34-38% in Murrah buffaloes during 2007-2011. Average EPA of elite KF
and Sahiwal cows and Murrah buffaloes ranged between 4492 and 5520 kg; between
2199 and 2440 kg and between 2339 and 2371 kg, respectively.

Two sets each of Sahiwal (11 bulls) and KF (17 bulls) and three sets of Murrah bulls
(43 bulls) were evaluated during the period. Out of these bulls, 4 Sahiwal, 5 KF and 3
Murrah bulls were selected as proven bulls with their EBVs ranging from 1641-1917
kg, 3228-4144 kg and 1972-2116 kg, respectively; while their superiority over herd
average ranged from 9.33-27.73%, 12.00-16.70% and 8.41-17.26%, respectively.
During 2007-2011, a total of 2152 KF and 2325 Murrah female progeny has born from
bulls under field conditions.

During the period, a total of 3,72,770 doses of frozen semen of Karan Fries, Sahiwal
and Murrah bulls were produced and 4,70,134 doses of frozen semen of three breeds
were disseminated (sold and supplied ) through ABRC, NDRI to various dairy
development agencies / institutes and farmers.

Higher accuracy of prediction (92%) of FL305DMY from the optimum equation
incorporating test day milk yields (35th, 65th, 125th, 185th and 275th day) revealed
that these test day milk yields can be used to predict FL305DMY with higher degree of
accuracy in Sahiwal cattle.

The relative efficiency of selection on the basis of part lactation milk yields over
FL305DMY was though lesser, yet comparable, in Sahiwal cattle. Selection on the
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basis of individual third month milk yield and cumulative 90 days milk yield was at
least 89% and 79% as effective as on the basis of FL305DMY.
The DFREML method was adjudged as the most efficient and accurate method of sire
evaluation among the four methods (least squares, simple regressed least squares
and BLUP) used in Sahiwal cattle. The single trait DFREML was more efficient than
multi trait DFREML for estimating the breeding value of Sahiwal sires for FL305DMY,
individual third month milk yield and cumulative 90 days milk yield.
Five models (EDF=Exponential decline function; PEF=Parabolic exponential function;
GF=Gamma type function; MLF=Mixed log function; IPF= Inverse polynomial function)
were used to fit lactation curve based on weekly test day milk yields in Sahiwal cattle.
The inverse polynomial function (IPF) was found to be the best fit (R2 value = 99.8%).
The growth curves up to 6 months of age were linear in nature in both male and female
Sahiwal calves. Average daily weight gain from birth to 6 months of age was
339.11g/day in female calves and 333.50 g/day in male calves. The growth bands
were constructed for male and female calves using 26 weeks body weight in Sahiwal
calves. These growth bands can be used as a criterion of selection of young calves at
an early age.
The lactation curve parameters of Quadratic cum log model (QCLM), Gamma function
(GF), Cobby Le Du model (CLDM), Polynomial regression function (PRF) and
Multiphasic logistic function (MLF) were estimated using 57233 WTDMY of first
lactation in Karan Fries cows for developing the best model of lactation curve. The
polynomial regression function was found to be the best lactation curve model followed
by quadratic cum log model based on coefficient of determination (R2) and root mean
square error (RMSE) for predicting weekly and monthly test day milk yield for first,
second, third and fourth lactation in Karan Fries cattle.
First lactation monthly test day milk yields were used to predict 305-day or less milk
yield using different sampling methods viz., centering date method (CDM), test interval
method (TIM) and sample day production method (SPM). The sample day production
method was found to be the best method for predicting 305-day or less milk yield in
Karan Fries cattle and can be used under field conditions.
The accuracy of prediction of 305-day or less milk yield from individual monthly test
day milk yield (MTDYs), monthly milk yield and cumulative monthly milk yield were
observed to be the best for MTDY-6 (62%), month-6 (70%) and 180-day cumulative
milk yields (75%) respectively.
Based on fitting of stepwise multiple regressions, the regression equation with 4
variables viz. MTDY 4, MTDY-6, MTDY- 9 and MTDY-2 was considered more
appropriate for prediction of first lactation 305-day milk yield with 86% accuracy and
6.79 percent error of prediction in 305-day milk yield.
The lactation curve models were developed for Murrah buffaloes using four functions
(Inverse quadratic polynomial, exponential, polynomial regression and mixed log
functions) based on weekly and monthly test day milk yield of buffaloes for developing
three and five parameters lactation curve models. The models can be used for
predicting weekly, monthly and total lactation milk yield in Murrah buffaloes in
organized and rural households.
The waiting period or days to first service should be 63 days for Murrah Buffaloes. The
daughters pregnancy rate (DPR) of Murrah buffalo has also been standardized. The
conversion of first service period to DPR 63 for Murrah buffalo should be DPR 63 =
0.0033 (274 – FSP).

The methodology for estimating Daily Breeding Values (DBVs) of Murrah buffaloes
based on test day first lactation milk yield records using Random Regression Models
(RRMs) has been standardized for genetic evaluation of buffaloes.
Project 2: Identification of Genetic Polymorphism for Performance Traits in Sahiwal
Cattle and Murrah Buffaloes
Achievements/Techniques developed:

Seven candidate genes namely: α S1-casein (CSN1S1); β - casein (CSN2); SRY;
Leptin; Lactoferrin; PIT-1 and Interleukin-8 (IL-8) were explored for DNA polymorphism
using SSCP and PCR-RFLP techniques in Sahiwal herd of NDRI. Out of which three
genes i.e. Lactoferrin; PIT-1 and Interleukin-8 (IL-8) were polymorphic and rest were
monomorphic.

Six SNPs in Promoter region and two SNPs in intronic region were found in Lactoferrin
gene in Sahiwal cattle. All SNPs were synonymous type.

Characterization of Lactoferrin gene revealed a total of 13 Putative transcription factors
binding sites (TFBS) in 1.041 kb 5’ flanking region of Sahiwal cattle. The 5’
untranslated region (5’ UTR) found to be 39 bases length and the exon 1 was identified
to be 82 bases length.

PCR-RFLP analysis of PIT-1 gene (1355 bp fragment containing exon 5, intron 5 and
exon 6) using Hinf 1 restriction enzyme in 230 Sahiwal Cattle exhibited three
genotypes. Frequency of allele A was 13.3% & allele B was 86.7%. Animals with AA
genotype yielded more milk (~25%) than AB and BB genotyped animals.

PCR-RFLP analysis of IL-8 gene (578 bp fragment from 3205-3783 nt containing exon
4 and 3’UTR) using Dra 1 restriction enzyme in 179 Sahiwal Cattle exhibited two
genotypes. Frequency of allele C was 84.6% & allele D was 15.4%. Animals with CD
(22/55=40%) genotype were found to be less susceptible to mastitis than CC animals.

Six candidate genes namely: Interleukin-8 (IL-8); Leptin; Lactoferrin; PIT-1; Prolactin
and TLR-4 were explored for DNA polymorphism using SSCP and PCR-RFLP
techniques in Murrah buffalo herd of NDRI. Out of three genes i.e. Prolactin;
Interleukin-8 (IL-8) and TLR 4 were polymorphic and rests were monomorphic.

PCR-RFLP analysis of IL-8 gene using Dra 1 restriction enzyme in 109 Murrah
buffaloes exhibited three (AA, AB and BB) genotypes. However, these genotypes
indicated non-significant association with incidence of mastitis in Murrah buffaloes.
Project 3: Molecular Characterization and Identification of Polymorphism in Mastitis
Related Genes in Sahiwal, Karan Fries Cattle and Murrah Buffaloes
Achievements/Techniques developed:
Factor XI gene in Sahiwal and Karan Fries cattle:

DNA polymorphism using PCR technique was carried out in 253 Sahiwal and 200
Karan Fries cattle to genotype the animals for FXI deficiency with reported primers to
amplify exon 12 (244 and/or 320 bp PCR products) of FXI gene. Genotyping of all the
animals revealed neither homozygous mutant nor heterozygous carrier individual. It is
concluded that studied animals of Sahiwal and KF cattle of NDRI are free from FXI
gene deficiency.
CARD 15 Gene in Sahiwal Cattle:

PCR-RFLP analysis of exon 12 of CARD 15 gene in 162 Sahiwal cattle using SacI and
PvuII restriction enzymes was carried out. Association of polymorphic pattern of Primer
2-SacI and Primer 5-PvuII with incidence of mastitis were found to be non- significant.

Seven nucleotide changes (SNPs) were found in the 3’UTR region of Exon 12, of this
four in contig 4 and one each in contig 1, 2 and 5.
TLR 4 Gene in Sahiwal Cattle:

PCR-RFLP analysis was done using three restriction enzyme Hinf I and AluI of TLR4
gene in 190 Sahiwal cattle. Hinf I RFLP revealed three CC, CD and DD genotypes. CC
genotype of primer 3.4 with Hinf I RE was susceptible (58.27%) to mastitis in Sahiwal
cattle.

Alu1-RFLP revealed polymorphism in primer 2 having AA, AB genotypes and primer
3.7 having AA, AB and BB genotypes. BB genotype of primer 3.7 with Alu I RE was
susceptible (60.00 %) to mastitis in Sahiwal cattle.

Total 7 SNPs were observed in exon 3 out of which one was non-synonymous SNP
causing amino acid substitution: Valine (V) to Isolucine (I) at template position 650.
CD14 gene in Sahiwal cattle:

PCR-RFLP analysis of Cluster of Differentiation (CD14) gene in 100 lactating Sahiwal
cattle was done using three restriction enzymes (HinfI, HaeIII and Hpy188I). CC
genotyped (Hpy188I- RFLP) and AA genotyped (HinfI-RFLP) animals were found less
susceptible to mastitis incidence.

Sixteen nucleotide changes (SNPs) were observed in CD14 gene in Sahiwal cattle
when compared with reference sequences of Bos taurus. Out of these SNPs four were
in coding region with synonymous mutation. Two SNPs were found heterozygous at
position 418 (A/C) and 2276 (C/T).
TLR 4 gene in Murrah buffaloes:

PCR-RFLP analysis of Toll like receptor 4 (TLR 4) with BsiHKA I RE in 102 randomly
selected lactating Murrah buffaloes (NDRI) were analyzed using nine set of primers.
Primer 3 and 7 revealed monomorphism exhibiting only BB genotype. Primer 8 and 9
revealed three genotypes. Primers 1, 2, 4, 5 and 6 of TLR4 gene did not have any
cutting site with BsiHKA I.

Chi-square analysis for establishing association of polymorphic patterns in TLR4BsiHKA I gene with incidence of mastitis in Murrah buffalo was non significant for
primer 9, however, it was found to be significant for primer 8 (P<0.01) and the study
indicates that animals with AA genotypes are more susceptible to mastitis as
compared to AB and BB genotypes with respect to TLR 4- Primer 8-BsiHKAI RFLP.
CARD 15 Gene in Murrah Buffalo:

Complete coding sequences of CARD 15 gene was characterized which spans 5105
bp consisting of twelve exons. Total 118 nucleotide changes were observed when
compared to Bos taurus. 87 of these changes were in coding region. In the 3’UTR, two
insertions of 9 and 7 bp and one deletion of 16 bp were found which seem to be
characteristics of the Murrah breed. At amino acid level, 18 changes were observed.

PCR-RFLP analysis was done using three restriction enzyme BsaHI, PvuII and SacI.
CARD15 gene in 150 Murrah buffalo. The association of polymorphic patterns with
incidence of mastitis was non-significant.
FEZL gene in Murrah Buffalo:

Complete coding sequences of FEZL gene in Murrah buffaloes was characterized. A
total of 14 changes were found, out of which 6 in intron 1; 5 in intron 3 and 3 in non
coding region of exon 4. The remarkable changes from the reference sequence were
deletion of three bases CCA at position 2600, an insertion of three bases TCT in intron
3 at position 3152-3154, 5 bases GAAAA after nucleotide position 4365 and a stretch
of 14 bases TAAACAGAATCTTA after nucleotide 4684 of Bos taurus sequence.

PCR-RFLP analysis using Dra I, Msp I and Taq I restriction enzymes revealed
polymorphism in FEZL gene in 100 lactating Murrah buffaloes. The polymorphic
pattern in P6-MspI was found to be significantly associated with incidence of mastitis.
Moreover, the animals with AA genotypes have been found to be more resistant to
mastitis as compared to AB and BB genotypes.
Project 4: Multiplication and dissemination of Tharparkar germplasm
Achievements/Techniques developed: The project was initiated in 2011. The germplasm is
being multiplied. New germplasm (semen/males) was introduced from outside sources (IVRI/
CCBF Suratgarh) to increase genetic variability in the Institute herd of Tharparakar cattle.
Project 5: Multi-trait evaluation of Karan Fries cattle for higher productivity and fertility
Achievements / techniques developed: Project has started in January, 2012 and data
collection is in progress.
Project 6: Fluorescent in situ hybridization (FISH) and associated techniques for
characterization of chromosomes for detection of genetical and reproductive problems in
cattle, buffalo and goats
Achievements/Techniques developed: The project approval and grant (Rs.31.93 lacs) was
received in June 2011 only. During the year equipments and other items were procured.
Research work has been initiated, findings are to come.
Project 7: Network Project on Buffalo Improvement - NDRI Center
Achievements / techniques developed:The project was monitored and bulls of different
centers were selected and tested in the herd. Murrah bulls of NDRI Center were declared as
Best Proven bulls under the project. Recorded highest milk yield of Murrah buffalo (25.1 Kg)
under Network Project of Buffalo Improvement at NDRI herd. Generated and maintained genetic
stock of elite Murrah buffaloes and created the various databases of Murrah buffalo genetic
resources.
The Waiting Period (WP) or Days to First Service (DFS) as standardized as 63 days for Murrah
buffaloes for better fertility. Developed optimum models for prediction of fertility (pregnancy rate)
in Murrah buffaloes, the research was recognized as Best M. V. Sc research work in Production
Group of Subjects at NDRI in 2011.
Project 8: Network Project on Buffalo Improvement - Field unit
Achievements/Techniques developed:

During the last 5 years (2007-12), as many as 11970 AIs were done with a conception
rate of 46.0%. A total of 4926 calves were born, out of which 2601 were males and 2325
were females.

A total of 166 daughters have completed the first lactation milk yield records and monthly
test day milk yield has been recorded for these cows belonging to different sets of bulls.
The 305-day milk yield will be predicted using these records to be used for sire
evaluation.

The multiple regression model developed for NDRI was applied in the field for prediction
of 305-day milk yield under different management systems comprising of different
buffalo herd sizes and practice of wallowing (regular or irregular)
Project 9: Indigenous breed project on Sahiwal cattle
Achievements/Techniques developed: The first set of 8 Sahiwal bulls has been put under
progeny testing in the germplasm and data recording units. The dam’s best yield of these bulls
ranged from 2503 (first lactation) – 3704 kg. A total of 2136 semen doses have been provided to
various data recording units. A total of 2015 AIs have been done in all the centres including
germplasm unit with the semen of these bulls till date and a total of 734 pregnancies have been
recorded. The overall average conception rate of 36.43% was observed in various herds. It
ranged from 25.70% (Pantnagar) to 41.50% (Lucknow). A total of 138 daughters have been
born at different herds, out of which 93 daughters were born at the five data recording centres
and 45 daughters were born at the germplasm unit. The overall conception rate was 27.96 per
cent at GADVASU, Ludhiana; 41.5 % at GLF, Lucknow; 38.80 % at GLF, Hisar; 25.70% at
GBPUAT Pantnagar and 26.71 % at Gaushala Bhiwani. The overall conception rate at the NDRI
Karnal was 40.68%.
A total of 168 calves have been born in the Sahiwal herd of NDRI Karnal, out of which 83 were
male calves, 77 were female calves and 8 were abnormal births (4 each male and female). The
percentage of abnormal calves was 4.60 in males, 4.76 in females with an overall average of
4.76%. The percentage of abnormal calves ranged from 0 – 16.67% in males calves and 0 –
14.29% in female calves, respectively.
The overall population means for age at first calving, first lactation total milk yield, first lactation
305 day or less milk yield, first lactation length, first peak yield, first dry period, first service
period, wet average and herd average at NDRI farm were 1190.33±23.30 days,
1760.39±144.99 kg, 1671.63±131.46 kg, 297.32±16.45 days, 9.46±0.72 kg, 155.78±20.97 days,
121.50±16.32 days, 387.95±11.32, 6.6±0.30 kg and 3.6±0.27 kg, respectively.