Making the Intermated B73 X MO17 mapping population

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Making the Intermated B73 X MO17 mapping
population of recombinant inbred lines (RILs)
Mo17
B73
X
Single F2 plant was selfed
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Grow up 200 plants, random mating
Illustration of the genotype of 6 of those 200
plants. Recombination during meiosis results in
the exchange of chromosome segments
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Select 100 ears, pick 5 kernels from each ear.
Put in a bag, shake, plant, more random matings
(2nd generation). Repeat, (repeat.)
From these lines, generate Recombinant Inbred
lines by repeated selfing (5x or more)
And Tahdah! the Recombinant Inbred mapping
population
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Finding quantitative trait loci (QTLs)

• You test your population of plants for the
  presence of a phenotype (e.g. leaf size) and you
  determine the statistical likelihood that each
  molecular marker is associated with the trait.
  This gives you a LOD score (logarithm of the odds
  that they are associated). You plot LOD scores
  along the chromosome, and where it is highest you
  have a QTL locus (one or more genes) that
  determines your phenotype.
• In the example shown, Antirrhinum majus
  (snapdragon) has 4 QTLs for leaf size.

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How do we get pairing of homoeologous chromosomes?
Wild sex in this example means inter- specific
crossing or hybridization. Homologous
chromosomes readily pair during meiosis, but
homoeologous Chromosomes do not. Homoeologous
means partially homologous, usually
indicating some original ancestral homology.
Pairing is prevented by Certain genes that
evolve as part of speciation. Can those genes be
identified and then knocked out?
What we need is a little more
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Breaking the cereal species barrierpairing of
homoeologous chromosomes

• Bread wheat contains three closely related
  genomes A, B and D. Chromosome pairing during
  meiosis is confined to strict homologues, despite
  the co-existence in the genome of homoeologous
  chromosomes. This control maintains the integrity
  of the three genomes. The genetic control of
  chromosome pairing in wheat is dependent on a
  series of genes that suppress and promote
  homoeologous pairing (Ph genes). The strongest
  effect on pairing is associated with a gene (or
  genes) at the Ph1 locus) that suppresses
  homoeologous chromosome pairing within the
  polyploid wheat genome. In the absence of Ph1,
  homoeologous recombination can occur between
  wheat chromosomes and those from related species
  or genera. An X-ray-induced deletion at the Ph2
  locus, ph2a, and a chemically induced mutant,
  ph2b, have demonstrated that removal of the Ph2
  gene induces an intermediate level of
  homoeologous chromosome pairing in wheat hybrids
  with alien species but does not affect chromosome
  pairing in wheat itself. These observations
  suggest that Ph2 will be a valuable resource for
  the introgression of alien genes from related
  species into bread wheat, with minimum disruption
  of endogenous homologous chromosome pairing.

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Rice flower
1. Put pollen from Oryza glaberrima on the pistil
of Oryza sativa, and allow embryo to develop.
Collect the seeds that are formed with very low
frequency.
Male stamens

2. Backcross the progeny multiple times to O.
sativa so that you end up with a plant that is
85 Sativa and 15 Glaberrima.
Female pistil
AA X BB A (pollen) B (egg) --gt A (50)B
(50) Mostly infertile and very few seeds are
formed After back-crossing --gt A(85)B(15)
highly fertile plant
Such a hybrid does not form in Nature, first
because the two species grow on different
continents, but second because the pollination is
nearly infertile. It combines genes from two
different species, but is not a GMO.
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Inter-specific hybridization Nerica, an upland
rice for Africa.
Asian rice
African rice
Nerica rice

• Oryza sativa (Asian upland rice) non-shattering,
  resistant to lodging, high yield potential
• Oryza glaberrima (African rice) drought
  tolerant, disease resistant, weed-suppressing
• Nerica rice combines the best of both species.

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Wide crossing of wheat and rye requires embryo
rescue and chemical treatment to double the
number of chromosomes.
Triticale
http//gnome.agrenv.mcgill.ca/breeding/tritical.ht
m
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Triticale, a new cereal created in the
lab.Triticale, a cross between wheat and rye,
was produced by embryo rescue of the product of
fertilization and a chemically induced doubling
of the chromosomes. Embryo rescue becomes
necessary when fertile offspring is never
produced by an interspecific cross.
Triticale is now grown all over the world
Wheat, triticale and rye
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Soluble solids are the holy grail of the tomato
processing industry, because the most expensive
part of making tomato sauce/paste is evaporating
the water. Useful yield is determined by soluble
solids. Roma tomatoes have high soluble solids.
Roma tomatoes have less water
Refractometer to measure BRIX value
Plant breeders and genetic engineers focus on
soluble solids (sucrose and other soluble
molecules), which are measured as the BRIX value
of the tomato juice.
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Zamir and colleagues at the Hebrew University
made RILs between Solanum lycopersicum (domestic
tomato) and Solanum pennellii. They identified 25
QTLs for soluble solids measured as Brix value.
One QTL improved Brix by 10-20. Mapping showed
it to map to a chromosome region that encodes a
fruit specific invertase. Fine mapping narrowed
it down to a SNP in a 484 bp region of the
invertase. In one specific place S. pennellii
has a D (Asp) - in common with invertases from
carrot, tobacco, potato and pea, but the S.
lycopersicum invertase has an E (Glu)The enzyme
has a higher affinity (lower Km) for sucrose and
is more efficient at unloading sucrose in the
fruit.Science, 305 1786-9 (2004)
Make recombinant inbred lines (RILs) and
identify quantitative trait loci (QTLs) for
Brix value.
Glu
Asp
Brix refractive index and measures mostly
sugars.