Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening.
BACKGROUND
Kiwifruit (Actinidia spp.) are a relatively new, but economically important crop grown in many different parts of the world. Commercial success is driven by the development of new cultivars with novel consumer traits including flavor, appearance, healthful components and convenience. To increase our understanding of the genetic diversity and gene-based control of these key traits in Actinidia, we have produced a collection of 132,577 expressed sequence tags (ESTs).


RESULTS
The ESTs were derived mainly from four Actinidia species (A. chinensis, A. deliciosa, A. arguta and A. eriantha) and fell into 41,858 non redundant clusters (18,070 tentative consensus sequences and 23,788 EST singletons). Analysis of flavor and fragrance-related gene families (acyltransferases and carboxylesterases) and pathways (terpenoid biosynthesis) is presented in comparison with a chemical analysis of the compounds present in Actinidia including esters, acids, alcohols and terpenes. ESTs are identified for most genes in color pathways controlling chlorophyll degradation and carotenoid biosynthesis. In the health area, data are presented on the ESTs involved in ascorbic acid and quinic acid biosynthesis showing not only that genes for many of the steps in these pathways are represented in the database, but that genes encoding some critical steps are absent. In the convenience area, genes related to different stages of fruit softening are identified.


CONCLUSIONS
This large EST resource will allow researchers to undertake the tremendous challenge of understanding the molecular basis of genetic diversity in the Actinidia genus as well as provide an EST resource for comparative fruit genomics. The various bioinformatics analyses we have undertaken demonstrates the extent of coverage of ESTs for genes encoding different biochemical pathways in Actinidia.
Crowhurst
Ross N
RN
The Horticultural and Food Research Institute of New Zealand, PB 92169, Auckland, New Zealand. RCrowhurst@hortresearch.co.nz
Gleave
Andrew P
AP
MacRae
Elspeth A
EA
Ampomah-Dwamena
Charles
C
Atkinson
Ross G
RG
Beuning
Lesley L
LL
Bulley
Sean M
SM
Chagne
David
D
Marsh
Ken B
KB
Matich
Adam J
AJ
Montefiori
Mirco
M
Newcomb
Richard D
RD
Schaffer
Robert J
RJ
Usadel
Björn
B
Allan
Andrew C
AC
Boldingh
Helen L
HL
Bowen
Judith H
JH
Davy
Marcus W
MW
Eckloff
Rheinhart
R
Ferguson
A Ross
AR
Fraser
Lena G
LG
Gera
Emma
E
Hellens
Roger P
RP
Janssen
Bart J
BJ
Klages
Karin
K
Lo
Kim R
KR
MacDiarmid
Robin M
RM
Nain
Bhawana
B
McNeilage
Mark A
MA
Rassam
Maysoon
M
Richardson
Annette C
AC
Rikkerink
Erik Ha
EH
Ross
Gavin S
GS
Schröder
Roswitha
R
Snowden
Kimberley C
KC
Souleyre
Edwige J F
EJ
Templeton
Matt D
MD
Walton
Eric F
EF
Wang
Daisy
D
Wang
Mindy Y
MY
Wang
Yanming Y
YY
Wood
Marion
M
Wu
Rongmei
R
Yauk
Yar-Khing
YK
Laing
William A
WA
D029042:Actinidia / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism / Q000502:physiology*; D000328:Adult; D000485:Allergens / Q000235:genetics; D001205:Ascorbic Acid / Q000235:genetics / Q000378:metabolism; D002648:Child; D003062:Codon; D016384:Consensus Sequence; D030541:Databases, Genetic; D004952:Esters / Q000378:metabolism; D020224:Expressed Sequence Tags; D005638:Fruit / Q000235:genetics / Q000254:growth & development* / Q000378:metabolism; D017343:Genes, Plant / Q000235:genetics; D005819:Genetic Markers; D006801:Humans; D018895:Microsatellite Repeats; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D010802:Phylogeny; D010858:Pigmentation / Q000235:genetics*; D010860:Pigments, Biological / Q000096:biosynthesis / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D011801:Quinic Acid / Q000378:metabolism; D017421:Sequence Analysis; D013649:Taste; D013729:Terpenes / Q000378:metabolism
D000485:Allergens; D003062:Codon; D004952:Esters; D005819:Genetic Markers; D010860:Pigments, Biological; D013729:Terpenes; D011801:Quinic Acid; D001205:Ascorbic Acid