lecture 9: hybrid vigor...

Lecture 9:

Hybrid Vigor (Heterosis)

Michael Gore lecture notes

Tucson Winter Institute

version 18 Jan 2013

Breaking Yield Barriers for 2050

Phillips 2010 Crop Sci. 50:S-99-S-108

Phillips 2010 Crop Sci. 50:S-99-S-108

Hybrid maize is

a modern marvel!

Springer and Stupar 2007 Genome Res. 17:264-275

Heterosis is one of the least

understood biological

phenomena that has been

exploited by breeders to

increase the productivity

of domesticated species

Springer and Stupar 2007 Genome Res. 17:264-275

Maize Traits with Heterosis

Northern Flint, Modern CBD, Southern Dent

Photo: http://thescientistgardener.blogspot.com/2010/12/maize-is-machine.html

Reid

Yellow

Dent OPV

Lancaster

Surecrop

OPV

The Making of Corn Belt Dent

Lessons from Corn Belt Dent

Heterosis in maize has been known

since the early 1900s

Concept of heterotic patterns

developed in the 1960s and 1970s

Breeding for heterotic patterns has

resulted in increased divergence between

groups

Tracy and Chandler 2006 pp 219–233


Ha: CBD heterotic patterns are not the

result of historical or geographical

influences

Open-pollinated varieties and first cycle

inbreds did not show heterotic patterns,

thus markers would NOT have been

helpful to identify heterotic groups



CBD heterotic patterns were created by

breeders through trial and error

In the 1940s, breeders started

arbitrarily splitting the germplasm pool

into groups (odd vs. even numbered lines)

Genetic drift created initial divergence

in allele frequencies, which was enhanced

by selection


Genome-Wide Patterns in CBD

van Heerwaarden et al. 2012 PNAS 109:12420-12425

Investigated 400 lines from over nearly

a century of breeding with ~50k SNPs

Steady increase in genetic

differentiation and LD, allele frequencies

in total population are mostly constant

Modern heterotic groups are the

product of divergence from a

homogenous landrace (OPV) population



Detected very few signatures of

directional selection

Overall impact of directional selection

on genome-wide patterns was limited



Minimal evidence for any single line

disproportionately contributing favorable

alleles

Common alleles donated by a set of

representative but few ancestral lines

Selection and recombination of many

common alleles important…but what

about genetic drift?

Genetics of Heterosis

Dominance hypothesis – masking of unfavorable recessive alleles

in a heterozygote. Two or more loci are needed because the value of a

heterozygote at a single locus (d>a) does not exceed the value of the

superior parent.

If true, it should be possible to obtain an inbred that performs equally

as well as the best hybrid

Overdominance hypothesis – the heterozygote is superior over

either homozygote. Only a single locus (d>a) is needed to achieve

heterosis. Also, linkage is not needed to achieve heterosis.

If true, it should NOT be possible to obtain an inbred that performs

equally as well as the best hybrid

Bernardo 2002 Breeding for Quantitative Traits in Plants pp 243-246

Genetics of Heterosis

Pseudo-Overdominance hypothesis – repulsion phase linkage of

loci that show partial or complete dominance

The effects of two loci are difficult to separate if both are tightly

linked. If we did not know that two loci comprise a single linkage

block, we would incorrectly conclude that heterosis is due to

overdominance.

Pseudo-overdominance is similar to the two-locus dominance

hypothesis, with the exception that repulsion phase linkage is required

for pseudo-overdominance.

Bernardo 2002 Breeding for Quantitative Traits in Plants pp 243-246

Genetic Models for Heterosis

Birchler et al. 2006 PNAS 103:12957-12958

Repulsion Phase Linkage –

Superior A and B alleles create

a superior phenotype from

complementation

Allelic interactions –

Heterozygosity at the B locus

with two functional alleles

Complementation –

Slightly deleterious

homozygous a, b, c alleles

Hill-Robertson Effect

HR effect – linkage between sites

under selection reduces the overall

effectiveness of selection for finite

natural populations

Repulsion phase linkages among

favorable alleles will reduce the

effectiveness of selection

Hill and Robertson 1966 Genet. Res. 8:269-294

Hill-Robertson Effect

Favorable alleles have a higher chance

of being in repulsion phase in the

presence of low recombination

If these favorable alleles exhibit

dominance, then low recombination

regions should be under high selective

pressure to maintain heterozygosity

McMullen 2009 Science 325:737-740

Pericentromeric Regions

- within 10 cM on each side of the centromere position

- the rest of the chromosome regions

McMullen et al. 2009 Science 325:737-740 and Gore et al. Science 326:1115-1117




Residual heterozygosity increased 30%

in pericentromeric regions (P<0.0004)McMullen et al. 2009 Science





Residual heterozygosity increased 30%

in pericentromeric regions (P<0.0004)McMullen et al. 2009 Science


Residual heterozygosity and R are

inversely correlated (r2sp=0.35)

Diversity (π) and gene density had no

association with residual heterozygosity.

NC Design III

Comstock and Robinson 1948 Biometrics 4:254-266

Design III is a mating design for

partitioning the genetic variance into

additive and non-additive effects

Design III estimates the average level

of dominance of genes affecting traits

under investigation

Random sample of F2 individuals are

separately backcrossed to each of the two

inbred parents

QTL Mapping for Heterosis

Stuber et al. 2002 Genetics 132:823-839

Concluded overdominance (or pseudo-overdominance)

is a major cause of heterosis for grain yield.

Analyzed backcross

series separately

QTL Mapping for Heterosis

Cockerham and Zeng Genetics 143:1437-1456

Concluded dominance effects at multiple linked QTL

are a major cause of heterosis for grain yield.

Re-analyzed Stuber et

al. 2002 backcross series

together with new

statistical model

Fine Mapping of Heterosis QTL

Graham et al. 1997 Crop Sci. 37:1601-1610

Overdominant QTL on chr 5 was dissected by NILs

into two tightly, linked dominant effect QTL in repulsion

phase. Provides evidence for pseudo-overdominance.

Meta-QTL Analysis of Heterosis

Schön et al. 2010 TAG 120:321-332

Concluded pseudo-overdominance is a major cause of

heterosis in maize and no significant epistasis. Heterotic

QTL for grain yield mapped near low R pericentromeric

regions (i.e., likely repulsion phase)

lecture 9: hybrid vigor...

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