MADHYA PRADESH PASHU CHIKITSA VIGYAN VISHWA VIDYALAYA JABALPUR (M.

P)

MARKER ASSISTED SELECTION IN LIVESTOCK & POULTRY:

CURRENT STATUS & FUTURE PROSPECTS

PRESENTED BY:

Kush Shrivastava M.V.Sc & A.H

Department Of Animal Breeding & Genetics

College of Veterinary Science & Animal Husbandry

Introduction
Conventional selection based on individual records,

pedigree or performance.

progeny

performance

or

family

Can be termed as phenotypic selection. MAS make use of DNA segments/ QTLs for selection

Types of markers
Morphological Biochemical Cytological DNA-based and/or molecular

DNA Markers

Quantitative traits

Genotype

Phenotype

Environment

Quantitative Trait Loci

Region of DNA that is associated with a particular

phenotypic trait.

These QTLs are often found on different chromosomes.

Knowing the number of QTLs that explains variation in the

phenotypic trait tells us about the genetic architecture of a

trait.

Types of Genetic markers

Genetic markers are located on chromosomes, like the proverbial beads on a string.

No function and no impact on animal performance.

Easily identified in the laboratory.

Direct Genetic Marker G E N E S M A R K E R

Indirect Genetic Marker

G E N E S

M A R K E R S

Selection based on markers

Genes
Individual observation

Genes

Information from relatives

Phenotype

QTL

Environment

Estimated Breeding Value

Molecular Genetic Markers

Selection

Relationship between the markers and the genes of interest (Dekkers, 2004)
The molecular marker is located within the gene of interest.

The marker is in linkage disequilibrium (LD) with QTL

throughout the whole population

The marker is not in linkage disequilibrium with QTL

throughout the whole population.

Linkage Disequilibrium

- Indicates mutation

(Ardlie et al., 2002)

In Dairy cattle
Olsen et al. (2002) , detected QTL for milk production chromosomes

3, 5, 6, 11, 13, 18 and 20 in Norwegian dairy cattle.

Trait1 MY F% FY Chromosome Position Marker - interval 6 18 5 6 3 5 11 P% PY 6 13 18 20
1MY 2NS

F value 3.74 4.58 4.90 11.76 3.73 3.69 3.71 16.38 4.62 3.47 3.05

P chromosome 0.019 0.003 0.009 <107 0.014 0.018 0.014 <107 0.005 0.018 0.037

P genome2 NS 0.08 NS <105 NS NS NS <105 NS NS NS

37 39 120 41 14 115 83 41 32 79 66

FBN12-BM143 INRA121-BM7109 UW48-ETH152 FBN9-FBN13 FCGR3-EAL BM1819-UW48 HUJV174-ILSTS45 FBN9-FBN13 BMC1222-BMS1352 ILSTS2-EAC BMS2361-UWCA26

= milk yield, F% = fat percentage, FY = fat yield, P% = protein percentage, PY = protein yield. = not significant.

Across-family QTL results for milk production traits on bovine chromosome 6 in the Norwegian Dairy Cattle population. Markers are pointed out on the lower X-axis and map distances in cM from the centromere are shown on the upper X-axis. F-values are shown on the Y-axis.

Olsen et al. (2002)

In Sheep
Maddox et al. (2001) : developed medium-density linkage

map of the ovine genome.

Wool traits in sheep

Purvis and Franklin (2004) reviewed major genes and QTL

affecting wool production & quality.

Trait 1. Fiber diameter 2. Fiber diameter 3. Fiber diameter Breeds Peppin Merino Merino x Romney INRA 401 Description (Chromosome no.) Chro. 1 Marker KRTAP6 and KRTAP8 Linked but not named Chro. 6 Chro. 25 Chro. 11 Chro. 3 Chro. 7 Chro. 25 Segment OARE101 (20cM), Segment IDVGA8 to midpoint with IDVGA088 KRT1.2, B2A and B2c Segment BMC1009 OARVH34, Segment ILST005 (20cM), Segment IDGVA8 IDVGA088 Reference Parsons et al. (1994) Henry et al. (1998) Ponz et al. (2001)

4. Staple length 5. Staple length

Romney INRA 401

Rogers et al. (1994) Ponz et al. (2001)

 Bidinost et al. (2008) identified QTL affecting wool

production and wool quality in Merino sheep.

QTL for wool traits in Merino sheep
Chromosome
3 4 4 25 25 25

Trait
FD1 **,# GFW2 * CFW2 * YLD1 *,# YLD2 * CV_FD2 *

Position (cM)
201 28 43 39 50 53

CI (cM)
193 205 2335 41end Origin52 4752 51end

Family no.
5 7 4 5 3 2 1 7 1

Greasy fleece weight, GFW; clean fleece weight, CFW; yield, YLD; fiber diameter, FD and coefficient of variation of fiber diameter, CV _FD. Subscript 1, hogget 14 month of age; subscript 2, adult 23 month of age. Confidence interval of QTL position, CI. * p < 0.05 chromosome-wide significance. ** p < 0.01 chromosome-wide. # p < 0.05 genome-wide significance.

F-statistics profile from interval mapping of sheep chromosomes 3, 4 and 25. Bar on the left represent markers position on each chromosome . Subscript 1 = hogget 14 month of age; subscript 2 = adult 23 month of age. Chromosome-wide significance p = 0.05 ( ). Experimental-wide significance p = 0.05 ( ) and information content ().

- Fiber diameter - Greasy fleece weight - Clean fleece weight

- Yield 1 - Yield 2 - Coefficient of variation of fiber diameter Bidinost et al. (2008)

Carcass traits in sheep

Margawati et al. (2009) detected QTL affecting carcass

traits in backcross family of Indonesian Thin Tail Sheep.

QTL location and flanking markers for carcass traits.
Traits Carcass weight Chromosome 2* 14** 23* Carcass length 15* 17** 1* QTL Location (cM) 264 8 28 80 104 256 Flanking markers OARHH30 BMS1126 BMS2213 LSCV30 CSSM031 MCM136 IDVGA10 BM0848 BM7136 TGLA322 BM6506 URB030

Leg circumference 15*

17*

92
104

IDVGA10 BM0848
BM7136 TGLA322

*Significant effect (p<0.05), **highly significant effect (p<0.01). There was no significance for carcass chest circumference.

In Pigs
Roberta Davoli and Silvia Braglia (2008), reviewed the

advances in pig molecular genetics & summarized the main markers that are utilized in pig industry.
DNA marker/ Gene MC4R RN-/rn+ (PRKAG3) IGF2 Developer ISU/PIC INRA/Uppsala/Kiel; ISU/PIC Liege/Uppsala Trait DG/FC/Lean MQ First application 1998 1997/1999/2000 Reference Kim et al. (2000) Ciobanu et al. (2001); Milan et al. (2000) Jeon et al. (1999); Nezer et al. (1999); Van Laere et al. (2003) Knap et al. (2002) Ciobanu et al. (2001); Meyers et al. (2007) Plastow et al. (2003)

Lean

2002

MQ (several genes) CAST

PIC and ISU/PIC ISU/PIC

MQ MQ

2001 2003

RL, DA

PIC

RL, DA

2003

MQ: meat quality; FC: feed conversion; DG: daily gain; RL: reproductive longevity; ISU: Iowa State University; INRA: Institut National de la Recherche Agronomique, France.

 Ya-lan et al. (2007) evaluated the effect and profitability

of gene-assisted selection in pig breeding system.

Extra economic returns (RMB yuan) 100 sow Model QBLUP P0= 0.1 3230647.30 P0= 0.3 559532.72 P0= 0.5 86018.29 P0= 0.1 5599108.49 200 sow P0= 0.3 2243969.43 P0= 0.5 2231599.75 P0= 0.1 6726772.58 300 sow P0= 0.3 3453732.47 P0= 0.5 4955329.35

FBLUP

3768478.93

2414493.20

614107.34

5354031.78

476440.35

3306397.27

6367686.56

4132929.78

5012847.05

P0: The initial frequency of the QTLs favorable allele

In Chicken
Liu et al. (2007) mapped quantitative trait loci affecting

body weight and abdominal fat weight on chicken chromosome 1.

The linkage map of chromosome 1 of the Northeast Agricultural University (China) resource population.

The QTL locations for BW and abdominal fat traits.

Position (cM)1 Trait F- ratio Flanking markers
BW Body Weight, #

69
183 195 219 231 271 339 343 351

AFP
AFW BW5 # BW0 BW3 BW2 BW4 BW1 BW8

5.08
4.67 11.54** 3.92 4.01 4.51 11.43** 3.22 8.72*

MCW0010-MCW0106
LEI0068-MCW0297 MCW0297-LEI0146 LEI0146-MCW0018 LEI0146-MCW0018 MCW0018-MCW0058 ADL251-MCW0061 MCW0061-LEI0088 MCW0061-LEI0088

Numbers following body weight indicates age in weeks. CW Carcass weight;. AFW Abdominal Fat

Weight;. AFP Abdominal Fat %, expressed as percentage of BW 12.

523
528 534 534 536 548 548 550 550 551 553 555

BW8
BW9 BW11 BW12 CW BW6 AFP BW10 AFW BW7 BW4 BW5

6.94
14.29** 18.72** 28.12** 28.06** 11.61** 11.91** 9.14** 7.39* 19.23** 9.31** 6.19*

LEI0079-ADL328
LEI0079-ADL328 LEI0079-ADL328 LEI0079-ADL328 LEI0079-ADL328 ADL0328-ROS0025 ADL0328-ROS0025 ADL0328-ROS0025 ADL0328-ROS0025 ADL0328-ROS0025 ADL0328-ROS0025 ADL0328-ROS0025
Liu et al. (2007)
1QTL

positions relative to the genetic map of Northeast Agricultural University resource population . Suggestive linkage; *Chromosome wide significant, P < 0.05; **Chromosome wide significant, P < 0.01.

The F-ratio of QTL mapping for abdominal fat weight (AFW) and abdominal fat percentage (AFP). Triangles above the X-axis indicate the marker positions.

The F-ratio of QTL mapping for BW at 11 (BW11), BW at 12 wk (BW12), and carcass weight (CW).Triangles above the X-axis indicate the marker positions.

Liu et al. (2007)

MAS in commercial livestock & poultry population

Finding QTL Marker association: Biggest challenge in

commercial populations. Long generation interval, unavailability of inbred lines, cost of genotyping are other limiting factors in livestock species. Researches in poultry: Mostly on experimental poultry populations. Only existing example on commercial level - French Dairy Cattle MAS programme. Two major designs are used The Daughter Design & The Granddaughter Design (Weller et.al., 1990) .

DAUGHTER DESIGN

(Weller et al., 1990)

Only a single family is shown, although in practice several families will be analysed jointly. The sire is assumed to be heterozygous for a QTL and a linked genetic marker. The two alleles of the marker locus are denoted M and m, and the two alleles of the QTL are denoted A and a. Alleles of maternal origin are denoted by question marks.

GRAND - DAUGHTER DESIGN

(Weller et al., 1990)

The grandsire is assumed to be heterozygous for a QTL and a linked genetic marker. Only a single family is shown. The two alleles of the marker locus are denoted as M and m, and the two alleles of the QTL are denoted A and a. Alleles of maternal origin are denoted by question marks. Genotypes are not listed for the granddaughters because they were not genotyped.

The French MAS programme

Started in 2000 (Boichard et al., 2002).

14 chromosomal regions selected

-According to previous studies (mainly French QTL program). -Containing at least one QTL underlying production, milk. -Composition, mastitis resistance (SCS), female fertility traced with 45 microsatellite markers. Individual genotyped - 10,000 genotypes per year.

French MAS: The Starting Point

(Boichard et al., 2003)

French MAS: First Results

(2001- 2007)

60000 genotyped individuals

45 microsatellite markers (14 QTL regions ~20% of the

genome).
Most QTL confirmed: 30 to 40% of the genetic variance

is explained by 3-5 QTLs

8 traits evaluated each month (MAS BV)

Evaluation of efficiency of French MAS programme (Guillaume et al., 2008)

Reliabilities (R2) of classical polygenic EBV (POL) and MAS EBV (MAS) for male candidates from 2004 and 2006.
Trait Milk yield Fat yield Protein yield Fat content Protein content POL 0.294 0.281 0.254 0.313 0.214 April 2004 MAS 0.327 0.296 0.273 0.407 0.301 Difference + 0.033 + 0.015 + 0.019 + 0.094 + 0.087 POL 0.313 0.310 0.303 0.342 0.342 April 2006 MAS 0.361 0.373 0.341 0.453 0.418 Difference + 0.048 + 0.063 + 0.038 + 0.111 + 0.076

Reliabilities of classical polygenic EBV (POL) and marker assisted EBV (MAS) of candidates of 2004, depending on the status of their sires.
Trait Sires of candidates without genotyped progeny daughters POL MAS Difference 0.266 0.302 +0.036 0.255 0.263 +0.008 0.243 0.265 +0.022 0.269 0.384 +0.115 0.200 0.301 +0.101 Sires of candidates with genotyped progeny daughters POL MAS Difference 0.291 0.353 +0.062 0.277 0.312 +0.035 0.267 0.307 +0.040 0.304 0.476 +0.172 0.210 0.372 +0.162

Milk yield Fat yield Protein yield Fat content Protein content

Incorporating MAS in selection programmes

(Dekkers ,2004)

Current status & future prospects

The Animal Quantitative Trait Locus (QTL) database

(AnimalQTLdb) : - It is designed to house all publicly available QTL data on livestock animal species for easily locating and making comparisons within and between species. - The database tools are also added to link

the QTL data to other types of genome information, such

as RH maps, physical maps, and human genome maps.
(Zhi- Liang Hu et al., 2010)

Summary of the Animal QTLdb

Species Pig Cattle Chicken Sheep Number of QTL 6344 4682 2451 348 Number of publication 281 274 125 47 Number of traits 593 376 248 137

Total

13825

727

1354

(Source - Animal QTLdb, 13th release)

QTL on Cattle Chromosome X

DYST Dystocia (maternal), BSE Bovine Spongiform Encephalopathy, EY Milk Energy Yield, FY Milk Fat Yield, MSPD Milking speed, MY Milk Yield, NONR Non return Rate, PY Milk Protein yield, RLEGS Rear Leg Set, SB Still Birth (maternal).

Red QTL lines represent for significant and light blue QTL lines for suggestive statistical evidence. Green dots represents the QTL peak position.

 eQTL ( Expression QTL):

- Confidence intervals of many QTL are wide, possibly harbouring hundreds of genes. This is the major obstacle to finding causative mutations underlying any QTL identified.

- Fine mapping techniques and

positional cloning are costly.

 Combining

QTL

detection

programs

and

high

throughput

transcriptome data to elucidate biological pathways associated with complex traits and their underlying genetic determinants is known as "Genetical Genomics (GG)" or "Integrative Genomics.

Treats the expression level of each gene present on a microarray as a

quantitative trait and use genetic markers to identify genomic regions that regulate gene expression phenotypes. Such regions are named

eQTL (expression Quantitative Trait Loci).

(Mignon et al., 2009)

 Whole genome selection (WGS) :

Meuwissen

et

al.

(2001):

predicted total genetic value using genome-wide dense marker maps. Genes affecting most

economically important traits are distributed throughout the

genome.

 Whole genome resequencing:

- The entire genome sequence data can be used to predict

the genetic value of an individual for complex traits.

- Theo Meuwissen and Mike Goddard (2010) suggested the use of whole genome resequencing for accurate prediction of

genetic values for complex traits.

- Accuracies of prediction of genetic value were >40% increased relative to the use of dense ~ 30K SNP chips. At equal high density, the inclusion of the causative mutations yielded an extra increase of accuracy of 2.53.7%.