In silico polymorphism analysis for the development of simple sequence repeat and transposon markers and construction of linkage map in cultivated peanut.
BACKGROUND
Peanut (Arachis hypogaea) is an autogamous allotetraploid legume (2n = 4x = 40) that is widely cultivated as a food and oil crop. More than 6,000 DNA markers have been developed in Arachis spp., but high-density linkage maps useful for genetics, genomics, and breeding have not been constructed due to extremely low genetic diversity. Polymorphic marker loci are useful for the construction of such high-density linkage maps. The present study used in silico analysis to develop simple sequence repeat-based and transposon-based markers.


RESULTS
The use of in silico analysis increased the efficiency of polymorphic marker development by more than 3-fold. In total, 926 (34.2%) of 2,702 markers showed polymorphisms between parental lines of the mapping population. Linkage analysis of the 926 markers along with 253 polymorphic markers selected from 4,449 published markers generated 21 linkage groups covering 2,166.4 cM with 1,114 loci. Based on the map thus produced, 23 quantitative trait loci (QTLs) for 15 agronomical traits were detected. Another linkage map with 326 loci was also constructed and revealed a relationship between the genotypes of the FAD2 genes and the ratio of oleic/linoleic acid in peanut seed.


CONCLUSIONS
In silico analysis of polymorphisms increased the efficiency of polymorphic marker development, and contributed to the construction of high-density linkage maps in cultivated peanut. The resultant maps were applicable to QTL analysis. Marker subsets and linkage maps developed in this study should be useful for genetics, genomics, and breeding in Arachis. The data are available at the Kazusa DNA Marker Database (http://marker.kazusa.or.jp).
Kazusa DNA Research Institute, Kisarazu, Chiba, Japan. shirasaw@kazusa.or.jp
Kenta
K
Shirasawa
Padmalatha
P
Koilkonda
Koh
K
Aoki
Hideki
H
Hirakawa
Satoshi
S
Tabata
Manabu
M
Watanabe
Makoto
M
Hasegawa
Hiroyuki
H
Kiyoshima
Shigeru
S
Suzuki
Chikara
C
Kuwata
Yoshiki
Y
Naito
Tsutomu
T
Kuboyama
Akihiro
A
Nakaya
Shigemi
S
Sasamoto
Akiko
A
Watanabe
Midori
M
Kato
Kumiko
K
Kawashima
Yoshie
Y
Kishida
Mitsuyo
M
Kohara
Atsushi
A
Kurabayashi
Chika
C
Takahashi
Hisano
H
Tsuruoka
Tsuyuko
T
Wada
Sachiko
S
Isobe
D010367:Arachis / Q000235:genetics*; D002874:Chromosome Mapping; D004251:DNA Transposable Elements; D018744:DNA, Plant / Q000235:genetics; D008040:Genetic Linkage; D005819:Genetic Markers; D018895:Microsatellite Repeats; D011110:Polymorphism, Genetic; D040641:Quantitative Trait Loci
D004251:DNA Transposable Elements; D018744:DNA, Plant; D005819:Genetic Markers