“Biological Production and Biological Environment” field

Creation of the tomato chromosomal map Elucidation of
QTL genes responsible for fruit size

Achievement : Contribution to modern crop breeding throughresearch on development of molecular geneticanalysis

During the 1980s, Dr. Steven Tanksley was the first to make amajor breakthrough in this field. He was involved in research on
plant molecular genetics and selective breeding at New Mexico
State University (1981-1985) and Cornell University (1985
onwards). Using the Restriction Fragment Length Polymorphism(RFLP) method, which had been developed at the time, Dr. Tanksley undertook the challenge of creating “chromosomal maps” forthe tomato and rice crops, which mark the location of important
genes on DNA.
The RFLP method enables the analysis of a chromosome’s
characteristics on the “individual level” by the fragment lengthof DNA when it is cut using a restriction enzyme. This method
centered on the fact that when the base sequence is identical, thefragment length is also identical, and when the gene differed, thefragment length also differed.
First, Dr. Tanksley successfully created a chromosomal map oftomato plant by the RFLP method. He then analyzed the locationof fragments where length differed across individual plants (genemapping) and discovered six QTLs related to the fruit size oftomatoes.
When his research achievements were published in the “Nature”
in 1988, a ripple of excitement ran through researchers aroundthe world engaged in the study of selective breeding, whether foranimals or plants. His research paper revealed that, by regarding
QTLs related to important traits as “DNA markers,” the selectionof individuals during selective breeding could now be backed byscientific evidence. In recognition of his innovative research, Dr.
Tanksley was elected a member of the U.S. National Academy ofSciences in 1995.

Dr. Steven D. Tanksley (USA)
Born: April 7, 1954 (Age 61)
Professor Emeritus, Cornell University

Summary
Since the beginning of agriculture, mankind has practiced selective
breeding in search of crops with enhanced traits. For most of that time,the methods practiced relied on experience and intuition. From the1980s, however, rapid advancements in genomic analysis techniquesbrought about significant changes. The pioneering figure who continuously led this field was Dr. Steven Tanksley.
Dr. Tanksley created chromosomal maps of crops by molecular
genetic analysis and went on to identify genes that are related toagricultural productivity, such as fruit size, thereby developing agenomic analysis technique that is instrumental for selective breeding.
His research, which combines genetic information and breeding techniques, has contributed enormously to increasing selection accuracy
and reducing the amount of time required to breed new crop varieties.

Selective breeding, from reliance on experience and intuition
to application of molecular genetics
It is believed that agriculture began 10 to 20 thousand years ago.
Humans took their staple wild plants and began intentionally cultivating them as crops. Through a long course of trial and error, humans
bred diverse varieties of “crops” by selectively cultivating thoseindividual crops that had higher yields and were more resistant to diseases and pests. “Selective breeding,” in which superior individuals
are crossbred, was also developed.
Most traditional selective breeding relied on experience, intuitionand luck, but in the 19th century, a “scientific perspective” was brought
into this field. Gregor Johann Mendel revealed that when two strainsof pea plants were crossbred, traits (properties and characteristics of anorganism) inherited by the offspring followed a certain fixed pattern.
It’s famously known as “Mendel's laws of inheritance.”
Mendel’s laws led to the adoption of a scientific approach to selectivebreeding. His laws, however, only applied to traits related to genes that
determine “qualitative” differences amongst individuals, such as “thecolor of the peas being green/yellow” and “the peas being round or
wrinkled,” most of which were caused by single genes.
In contrast, many of the traits we desire in crops, such as “largersize,” “greater yields” and “faster flowering,” cannot be determinedin the “black and white” manner of qualitative traits. These traits
are determined by a complex interaction of multiple genes on thechromosome and environmental factors. Genes of this nature arecalled “Quantitative Trait Loci (QTL).”
Even into the 20th century, traits determined by QTL were being
selectively bred based only on experience and intuition. However,following the discovery of restriction enzymes which cut doublestranded DNA containing the genes, selective breeding entered a newera in the 1980s with rapid advancements in the molecular genetic
analysis of crops.

Application of DNA markers leads to realization of efficient
selective breedingThroughout the 1990s to 2000s, Dr. Tanksley continues to leadthe field of selective breeding and plant genetics. One of his research
themes was to elucidate which genes of wild plant species mankind
had taken advantage of in order to create the modern species.
For example, Dr. Tanksley points out in his paper that whencomparing the wild ancestor of tomatoes, which originated inSouth America, with the modern species, fruit size has increased
several hundred-fold. Dr. Tanksley conducted research in which
he crossbred tomatoes that differed in fruit size and mapped out
the major QTLs that determine tomato fruit size. As a result,
he revealed that the modern species with larger fruit size had adecreased amount of transcription in certain genes, whereas thewild species of tomatoes with smaller fruit size had a large amountof transcription. He believes that such variation occurred during
the process of cultivation by humans and was accelerated byintentional selection of larger fruit. Dr. Tanksley’s research also
covers a wide variety of themes such as the elucidation of genes
for increased resistance to diseases and pests.
Led by Dr. Tanksley’s research, selective breeding using DNAmarkers began to spread around the world. In Japan, where rice is thestaple crop, new varieties have been developed using DNA markers
that influence agriculturally important traits, such as “resistanceto diseases and pests like the rice blast fungus,” “cold tolerance,”“variations of heading time (early or late)” and “taste,” some ofwhich have turned out to be exceptionally successful breeds.
Today, one of the most important themes surrounding selective
breeding is the challenge of adapting to global warming. Mankind
will face serious food shortages if agriculture is unable to adapt to
the rapidly changing climate. Therefore, the prompt and precisedevelopment of species adapted to the warming climate is essential.
In facing this challenge, the “development and application of DNA
markers for breeding” (Marker Assisted Selection), led by Dr.
Tanksley, is playing a crucial role.
In this manner, Dr. Steven Tanksley’s research has brought us toa new age in breeding techniques, which are contributing towards
solutions such as the realization of a stable and increased productionof food, and have become one of the most important technologies
for mankind in building a prosperous future.

QTL

Quantitative Trait Loci
The gene cluster that
influences the height,
the yield, and the flowering
period of a crop (right)
Qualitative Trait Loci :Mendel's principles ofinheritance determines
whether peas will be “green/yellow” and “round/wrinkled”
Size of ears

12C

3B

D

LOD score; The statistical score that
estimate the positional relation of phenotype
to DNA marker.

BAArrows indicate QTL

CLOD score

QTLs are found across multiple chromosomes

The size of the circle indicatesthe contribution rate of eachgene to a quantitative trait.

Size of the whole crops

ADThreshold

123

Chromosomal Location

Genes with high contribution rates are selected by DNA markers

The DNA marker
that's strongly
influential in theimprovement ofcrops

P1 Positional informationof genes with highcontribution rate in achromosomal map
P2 (DNA marker)

A DNA marker
with littleinfluence

ParentsP1P2Strong WeakOffspring☆

☆

☆

☆ Offspring that carry strongly influential DNA marker

Selection of superior
offspring by DNAmarkers (MAS) : Allows
fast and accurate
determination of which
parent the offspring
inherited its chromosome
fragment from