1. Fall 2016 - HORT6033 Molecular Plant Breeding
Instructor: Ainong Shi

2. Fall 2016 - HORT6033 Molecular Plant Breeding
Lecture Week 8 (10/10/2016)
QTL Mapping
Examples

3. QTL Mapping Talk from Public
Genetic Mapping and QTL Analysis at
Module 9: Mapping Quantitative Trait Loci (QTL) – CTGN at Youtube:
Quantitative Trait Locus (QTL) Mapping by Eric Xing

4. Linkage Group, Linkage Map, Linkage Mapping, and QTL Mapping
A linkage map describes the linear order of markers (such as SSRs and SNPs) within a linkage group. A linkage map = a genetic map.
Genetic mapping (linkage mapping) means to build genetic map(s) with a set of markers (such as SSRs and/or SNPs). It can map only one genetic map or whole genome maps of a species.
Usually, what we say ‘conduct linkage mapping’ means we map a major gene of a trait to a genetic map (linkage group (LG) or chromosome).
What we say ‘conduct QTL mapping’ means we map a QTL (quantitative loci trait) to one LG (chromosome) or several LGs (chromosomes) M1 M1 M1
0.1cM
0.1cM
0.1cM M2 M2 M2
0.2cM
0.2cM
0.2cM M3 M3 M3
0.1cM
0.25cM
T1 (flower color)
0.25cM
0.15cM M4 M4 M4
0.1cM
0.1cM
0.1cM M6 M5 M6 LG
Linkage map
QTL mapping

5. Population Development Marker Implementation
QTL Mapping Procedure
White rust resistant
White rust susceptible X
Population Development
Phenotypic Data
Marker Implementation
Donor Screening
Data Analysis
QTL Mapping
Genotypic Data
QTL analysis: Single marker test, interval mapping (IM), composite interval mapping (CIM), and multiple-interval mapping (MIM) analysis are performed using Windows QTL Cart V2.5 and QGene and QTLNetworkv2.1.
SNP
LOD
R^2
R298331
8.753
0.378
R347577
6.972
0.315
R296495
6.766
0.307
Marker Identification
SNP markers
Molecular Breeding

6. QTL Mapping Procedure Population Development P1 x P2 F1 F2 … P1 x P2…… …… …… …… …… ……
F2:n
n >5 … X x X x X x X x X x X x X x X x X x X x X x X x
RILs
>=250 F2 individuals
>=250 F2:3 Families
Recombinant inbred lines

7. Some Points for Mapping Population
F2 is mainly used for mapping (1) major genes and (2) major QTLs. The phenotypic data are based on single plant in F2. If a trait such as yield can’t be used F2 for QTL mapping because its phenotyping is not reliable based on single plant.
F2:3 can be used for any trait, but it can be kept for re-use and also has the dominant effect.
RILs can be used for any trait and is the best one for re-use, but it takes years to develop.

8. QTL Mapping Procedure 2. Phonetic Traits and Phenotyping
Field: white rust in spinach
Greenhouse: cowpea bacterial blight

9. Traits Interests for Cowpea Breeding and Genetics
Agronomic traits: grain (seed) yield and forage (leave) yield, 100-seed weight and seed size, maturity day, and processing quality such as seed coat and recovery % imbedded
Morphologic traits:
Plant habit (erect, semiprostrate, prostrate)
Dry pod color (straw, green, purple, black, speckled, brown)
Pod placement (above foliage, foliage level, below foliage, and mixed)
Pod position (erect, pendant, mixed)
Seed pattern color (black, brown, blue, green, grey, purple, red, tan, cream, yellow)
Abio- and biotic (disease and pest) resistance/tolerance:
Cowpea wilt (Fusarium oxysporum f. sp. tracheiphilum) resistance
Cowpea Mosaic Virus resistance (CPMV)
Cowpea bacterial blight (CBB) resistance
Cowpea aphid tolerance
Root-knot nematode (RKN, Meloidogyne spp.) tolerance
Iron deficiency chlorosis (IDC) and low phosphorus efficiency
Salt, drought, and heat tolerance
Seed protein and sugar content
Images from google search
CPMV
CBB
Cowpea Wilt
Aphid
RKN

11. Example of phenotypic data distribution
Field
Combined
Greenhouse
Distribution of disease reaction to F2:3 families derived from a cross of MN0095 and M (Field: the data from the field experiment, and Greenhouse: from the greenhouse; and Combined: combined both field and greenhouse experiments.).

12. QTL Mapping Procedure 3. Genotyping - SNP
Motella/LA2823 Mi AAGTAGACGAGGTTAGTAAAAT
Mogeor/LA3471 Mi AAGTAGACGAGGTTAGTAAAAT
NY mi AAGTAGACGACGTTAGTAAAAT
LA3130 mi AAGTAGACGACGTTAGTAAAAT
Motella
Mogeor G G
NY07-464
LA3130 C C

13. Genome-wide SNP Discovery
DNA Extraction
Genotyping by sequencing (GBS)
ddRADseq
Whole genome sequencing (WGS)
Whole genome resequencing
SNP Discovery
Spinach Germplasm
Data Analysis

14. QTL Mapping Procedure 4. Data Analysis
We will use the example data to do QTL mapping using five tools: JoinMap, MSTmap, WinQTLCart, QGene, QTLNetwork, and Mapchart. JoinMap is used to create the genetic maps for the population; WinQTLCart, QGene, and QTLNetwork are used to conduct QTL analysis and identify SNP markers associated with the traits; and Mapchart is used to create a nice looking images for the QTL maps.
The tools web sites are:
JoinMap 4.1:
MSTmap:
WinQTLCart:
Qgene:
QTLNetwork 2:
Mapchart 2.2:
R/QTL:
Please download the software and the user manuals! And then install them to you computers.

15. QTL Mapping Procedure 4. Data Analysis 4-1 Construct of Genetic Maps
Tools: JoinMap, MASTmap
We use WinQTLCart to create the genetic maps (leaf figure)

16. QTL Mapping Procedure 4. Data Analysis 4-2 QTL mapping by WinQTLCart
QTLs on LG1, 4, and 20 from WinQTLCart

17. QTL Mapping Procedure 4. Data Analysis 4-3 QTL mapping by Qgene
QTLs on LG1, 4, and 20 from QGene

18. QTL Mapping Procedure
4. Data Analysis
4-4 QTL mapping by QTLnetwork

19. QTL Mapping Procedure 4. Data Analysis 4-5 Draw QTL mapping
figures by Mapchart

20. QTL Mapping Procedure 5. SNP Identification SNP marker Expt
R-square (%)
QTL M M
Field
35.44
QTL1 + QTL2 Gh
41.52
combined
38.82 M
28.33
QTL1
35.02
31.38
5.29
QTL2
11.76
7.95