Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid
Reexamination Certificate
2001-06-06
2004-06-01
Horlick, Kenneth R. (Department: 1637)
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving nucleic acid
C435S410000, C435S468000, C436S094000
Reexamination Certificate
active
06743580
ABSTRACT:
TECHNICAL FIELD
This invention relates to using molecular and evolutionary techniques to identify polynucleotide and polypeptide sequences corresponding to commercially or aesthetically relevant traits in domesticated plants and animals.
BACKGROUND ART
Humans have bred plants and animals for thousands of years, selecting for certain commercially valuable and/or aesthetic traits. Domesticated plants differ from their wild ancestors in such traits as yield, short day length flowering, protein and/or oil content, ease of harvest, taste, disease resistance and drought resistance. Domesticated animals differ from their wild ancestors in such traits as fat and/or protein content, milk production, docility, fecundity and time to maturity. At the present time, most genes underlying the above differences are not known, nor, as importantly, are the specific changes that have evolved in these genes to provide these capabilities. Understanding the basis of these-differences between domesticated plants and animals and their wild ancestors will provide useful information for maintaining and enhancing those traits. In the case crop plants, identification of the specific genes that control for desired traits will allow direct and rapid improvement in a manner not previously possible.
Although comparison of homologous genes or proteins between domesticated species and their wild ancestors may provide useful information with respect to conserved molecular sequences and functional features, this approach is of limited use in identifying genes whose sequences have changed due to human imposed selective pressures. With the advent of sophisticated algorithms and analytical methods, much more information can be teased out of DNA sequence changes with regard to which genes have been positively selected. The most powerful of these methods, “K
A
/K
S
,” involves pairwise comparisons between aligned protein-coding nucleotide sequences of the ratios of
nonsynonymous
nucleotide
substitutions
per
nonsynonymous
site
(
K
A
)
synonymous
substitutions
per
synonymous
site
(
K
S
)
(where nonsynonymous means substitutions that change the encoded amino acid and synonymous means substitutions that do not change the encoded amino acid). “K
A
/K
S
-type methods” includes this and similar methods.
These methods have already been used to demonstrate the occurrence of Darwinian (i.e., natural) molecular-level positive selection, resulting in amino acid differences in homologous proteins. Several groups have used such methods to document that a particular protein has evolved more rapidly than the neutral substitution rate, and thus supports the existence of Darwinian molecular-level positive selection. For example, McDonald and Kreitman (1991)
Nature
351:652-654, propose a statistical test of neutral protein evolution hypothesis based on comparison of the number of amino acid replacement substitutions to synonymous substitutions in the coding region of a locus. When they apply this test to the Adh locus of three Drosophila species, they conclude that it shows instead that the locus has undergone adaptive fixation of selectively advantageous mutations and that selective fixation of adaptive mutations may be a viable alternative to the clocklike accumulation of neutral mutations as an explanation for most protein evolution. Jenkins et al. (1995)
Proc. R. Soc. Lond. B
261:203-207 use the McDonald & Kreitman test to investigate whether adaptive evolution is occurring in sequences controlling transcription (non-coding sequences).
Nakashima et al. (1995)
Proc. Natl. Acad. Sci USA
92:5606-5609, use the method of Miyata and Yasunaga to perform pairwise comparisons of the nucleotide sequences of ten PLA2 isozyme genes from two snake species; this method involves comparing the number of nucleotide substitutions per site for the noncoding regions including introns (K
N
) and the K
A
and K
S
. They conclude that the protein coding regions have been evolving at much higher rates than the noncoding regions including introns. The highly accelerated substitution rate is responsible for Darwinian molecular-level evolution of PLA2 isozyme genes to produce new physiological activities that must have provided strong selective advantage for catching prey or for defense against predators. Endo et al. (1996)
Mol. Biol. Evol.
13(5):685-690 use the method of Nei and Gojobori, wherein d
N
is the number of nonsynonymous substitutions and d
S
is the number of synonymous substitutions, for the purpose of identifying candidate genes on which positive natural selection operates. Metz and Palumbi (1996)
Mol. Biol. Evol.
13(2):397-406 use the McDonald & Kreitman (supra) test as well as a method attributed to Nei and Gojobori, Nei and Jin, and Kumar, Tamura, and Nei; examining the average proportions of P
n
, the replacement substitutions per replacement site, and P
s
, the silent substitutions per silent site, to look for evidence of positive selection on binding genes in sea urchins to investigate whether they have rapidly evolved as a prelude to species formation. Goodwin et al. (1996)
Mol. Biol. Evol.
13(2):346-358 uses similar methods to examine the evolution of a particular murine gene family and conclude that the methods provide important fundamental insights into how selection drives genetic divergence in an experimentally manipulatable system. Edwards et al. (1995) use degenerate primers to pull out MHC loci from various species of birds and an alligator species, which are then analyzed by the Nei and Gojobori methods (d
N
:d
S
ratios) to extend MHC studies to nonmammalian vertebrates. Whitfield et al. (1993) Nature 364:713-715 use K
A
/K
S
analysis to look for directional selection in the regions flanking a conserved region in the SR Y gene (that determines male sex). They suggest that the rapid evolution of SRY could be a significant cause of reproductive isolation, leading to new species. Wettsetin et al. (1996)
Mol. Biol. Evol
13(1):56-66 apply the MEGA program of Kumar, Tamura and Nei and phylogenetic analysis to investigate the diversification of MHC class I genes in squirrels and related rodents. Parharn and Ohta (1996)
Science
272:67-74 state that a population biology approach, including tests for selection as well as for gene conversion and neutral drift are required to analyze the generation and maintenance of human MHC class I polymorphism. Hughes (1997)
Mol. Biol. Evol.
14(1):1-5 compared over one hundred orthologous immunoglobulin C2 domains between human and rodent, using the method of Nei and Gojobori (d
N
:d
S
ratios) to test the hypothesis that proteins expressed in cells of the vertebrate immune system evolve unusually rapidly. Swanson and Vacquier (1998)
Science
281:710-712 use d
N
:d
S
ratios to demonstrate concerted evolution between the lysin and the egg receptor for lysin and discuss the role of such concerted evolution in forming new species (speciation). Messier and Stewart (1997)
Nature
385:151-154, used K
A
/K
S
to demonstrate positive selection in primate lysozymes.
The genetic changes associated with domestication have been most extensively investigated in maize (com) (Dorweiler (1993)
Science
262:232-235). For maize, (
Zea
ssp.
mays mays
), a smaller number of single-gene changes apparently accounts for all the differences between our present domesticated maize plant and its wild ancestor, teosinte (
Zea mays
ssp
paruiglumis
) (Dorweiler, 1993). QTL (quantitative trait locus) analysis has demonstrated (Doebley (1990)
PNAS USA
87:9888-9892) that no more than fifteen genes control traits of interest in maize and explain the profound difference in morphology between maize and teosinte (Wang (1999)
Nature
398:236-239).
Importantly, a similarly small number of genes may control traits of interest in other grass-derived crop plants, including rice, wheat, millet and sorghum (Paterson (1995)
Science
2
Messier Walter
Sikela James M.
Evolutionary Genomics LLC
Horlick Kenneth R.
Swanson & Bratschun LLC
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